Is RPS7 p.Ser34= (c.102G>A) pathogenic?

RPS7 p.Ser34= (c.102G>A) is classified Likely benign in RPS7 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-12-05). Ultra-rare (popmax 0.0567%, amr); Associated with Diamond-Blackfan anemia.

What condition is associated with RPS7 p.Ser34= (c.102G>A)?

RPS7 p.Ser34= (c.102G>A) is associated with Diamond-Blackfan anemia, Diamond-Blackfan anemia 8 (ClinVar).

How common is RPS7 p.Ser34= (c.102G>A) in the general population?

RPS7 p.Ser34= (c.102G>A) is ultra-rare (popmax 0.0567%, amr) (gnomAD).

How is Diamond-Blackfan anemia inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

RPS7 p.Ser34=

c.102G>A · rs754617897 · VCV701730

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0567%, amr)

Conditions

Diamond-Blackfan anemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.005	GERP -4.3, phastCons 0.64
Overall
CADD	11.77	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0567% Admixed American · 34/59,968 alleles

Filtering AF 0.0417% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0365%

Overall 0.00347% 56/1,611,936 alleles · ultra-rare exomes 42/1,459,726 · genomes 14/152,210 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0567%	1,764
Remaining individualsnot grpmax-eligible	0.00481%	20,771
European (non-Finnish)	0.00153%	65,542
African / African-American	0.00134%	74,878

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: RPS7
Protein: p.Ser34=
Coding: c.102G>A
MANE Select: NM_001011
dbSNP: rs754617897
Type: single nucleotide variant
Location: chr2:3575843 (GRCh38)
Gene constraint: LOEUF 0.317 · pLI 1.00 · ClinGen HI 2/3 (gnomAD)
Structure: AlphaFold pLDDT 87.04 · 182 PDB
Residue 34: a turn

Full RPS7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Diamond-Blackfan anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Diamond-Blackfan anemia 8

For Diamond-Blackfan anemia (Orphanet):

Inheritance: Autosomal dominant
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

RPS7 c.75+1G>A Pathogenic ★★ same condition
RPS7 c.356+6T>C Uncertain significance ★★ same condition
RPS7 c.-27C>T Uncertain significance ★★ same condition
RPS7 p.Ala26Val Uncertain significance ★★ ⚠ same condition
RPS7 p.Ala38Val Uncertain significance ★★ ⚠ same condition
RPS7 p.Arg145His Uncertain significance ★★ ⚠ same condition
RPS7 p.Arg152Pro Uncertain significance ★★ ⚠ same condition
RPS7 p.Asn12Ser Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/rps7-p-ser34 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown