Is CDA p.Ala70= (c.210T>C) pathogenic?

CDA p.Ala70= (c.210T>C) is classified Benign in CDA (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-10). Rare (popmax 0.49%, eas).

How common is CDA p.Ala70= (c.210T>C) in the general population?

CDA p.Ala70= (c.210T>C) is rare (popmax 0.49%, eas) (gnomAD).

CDA p.Ala70=

c.210T>C · rs76249360 · VCV737822

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.49%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.2	GERP -4.8
Overall
CADD	3.241	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.49% East Asian · 220/44,878 alleles

Filtering AF 0.437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.417%

Overall 0.109% 1,763/1,614,078 alleles · rare exomes 1,502/1,461,728 · genomes 261/152,350 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	1.78%	56
East Asiangrpmax	0.49%	204
Ashkenazi Jewishnot grpmax-eligible	0.206%	485
Remaining individualsnot grpmax-eligible	0.125%	801
Middle Eastern	0.033%	3,030
European (non-Finnish)	0.0219%	4,556
South Asian	0.00439%	22,759

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CDA
Protein: p.Ala70=
Coding: c.210T>C
MANE Select: NM_001785
dbSNP: rs76249360
Type: single nucleotide variant
Location: chr1:20604983 (GRCh38)
Gene constraint: LOEUF 0.955 · pLI 0.08 (gnomAD)
Structure: AlphaFold pLDDT 94.06 · 1 PDB
Residue 70: the cmp/dcmp-type deaminase domain; an α-helix

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

Similar variants

CDA p.Pro61= Benign ★★ same type
CDA p.Gln92His Uncertain significance ★ ⚠ same type
CDA p.Gly39Ala Uncertain significance ★ ⚠ same type
CDA p.Ile87Leu Uncertain significance ★ ⚠ same type
CDA p.Ile96Val Uncertain significance ★ ⚠ same type
CDA p.Met117Ile Uncertain significance ★ ⚠ same type
CDA p.Pro120Leu Uncertain significance ★ ⚠ same type
CDA p.Thr123Met Uncertain significance ★ ⚠ same type

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/cda-p-ala70 (accessed [today's date]).

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