Is BLVRB p.His49= (c.147C>T) pathogenic?

BLVRB p.His49= (c.147C>T) is classified Likely benign in BLVRB (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-31). Very rare (popmax 0.00942%, nfe).

How common is BLVRB p.His49= (c.147C>T) in the general population?

BLVRB p.His49= (c.147C>T) is very rare (popmax 0.00942%, nfe) (gnomAD).

BLVRB p.His49=

c.147C>T · rs747352017 · VCV710783

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00942%, nfe)

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 -1.6	GERP -2.6
Overall
CADD	1.664	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00942% European (non-Finnish) · 111/1,178,262 alleles

Filtering AF 0.00792% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00745%

Overall 0.00733% 118/1,608,998 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00942%	10,615
Finnishnot grpmax-eligible	0.00476%	21,028
Remaining individualsnot grpmax-eligible	0.00321%	31,115
Admixed American	0.00168%	59,400
South Asian	0.00111%	89,980

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: BLVRB
Protein: p.His49=
Coding: c.147C>T
MANE Select: NM_000713
dbSNP: rs747352017
Type: single nucleotide variant
Location: chr19:40458478 (GRCh38)
Gene constraint: LOEUF 1.718 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.71 · 23 PDB
Residue 49: a β-strand

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

Similar variants

BLVRB p.His49Asp Uncertain significance ★ ⚠ same residue
BLVRB p.Arg140Gly Likely benign ★★ same type
BLVRB p.Arg46Gln Likely benign ★★ same type
BLVRB p.Thr84= Benign ★★ same type
BLVRB p.Ala162Val Uncertain significance ★ ⚠ same type
BLVRB p.Ala21Thr Uncertain significance ★ ⚠ same type
BLVRB p.Ala26Thr Uncertain significance ★ ⚠ same type
BLVRB p.Ala7Val 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/blvrb-p-his49 (accessed [today's date]).

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