rs2774440

Variant names:

• chr13-111577767-T-C
• rs2774440

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.583 in 151,836 control chromosomes in the GnomAD database, including 25,967 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.58 (25967 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.583 AC: 88402 AN: 151718 Hom.: 25925 Cov.: 31

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.476

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.564

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.583 AC: 88507 AN: 151836 Hom.: 25967 Cov.: 31 AF XY: 0.582 AC XY: 43166 AN XY: 74178

African (AFR) AF: 0.646 AC: 26745 AN: 41410

American (AMR) AF: 0.536 AC: 8179 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1852 AN: 3470

East Asian (EAS) AF: 0.533 AC: 2735 AN: 5128

South Asian (SAS) AF: 0.477 AC: 2291 AN: 4806

European-Finnish (FIN) AF: 0.632 AC: 6666 AN: 10540

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38166 AN: 67924

Other (OTH) AF: 0.564 AC: 1186 AN: 2104

Alfa AF: 0.562 Hom.: 38194

Bravo AF: 0.582

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.6
DANN	Benign	0.43
PhyloP100		0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2774440; hg19: chr13-112230114;