rs4779937

Variant names:

• chr15-31895792-T-C
• rs4779937

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 0.513 in 151,810 control chromosomes in the GnomAD database, including 20,996 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 0.51 (20996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 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: 0.513 AC: 77872 AN: 151690 Hom.: 20975 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.513 AC: 77924 AN: 151810 Hom.: 20996 Cov.: 31 AF XY: 0.512 AC XY: 37974 AN XY: 74236

African (AFR) AF: 0.412 AC: 17016 AN: 41344

American (AMR) AF: 0.489 AC: 7456 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.526 AC: 1826 AN: 3470

East Asian (EAS) AF: 0.155 AC: 800 AN: 5158

South Asian (SAS) AF: 0.416 AC: 1998 AN: 4806

European-Finnish (FIN) AF: 0.633 AC: 6677 AN: 10554

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40310 AN: 67920

Other (OTH) AF: 0.527 AC: 1110 AN: 2108

Alfa AF: 0.551 Hom.: 39965

Bravo AF: 0.498

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.82
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs4779937; hg19: chr15-32187995;