rs1403937

Variant names:

• chr7-57280415-C-T
• rs1403937

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 0.465 in 151,960 control chromosomes in the GnomAD database, including 16,877 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 0.47 (16877 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.53 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: 0.465 AC: 70650 AN: 151840 Hom.: 16877 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.458

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

GnomAD4 genome AF: 0.465 AC: 70671 AN: 151960 Hom.: 16877 Cov.: 32 AF XY: 0.466 AC XY: 34595 AN XY: 74254

African (AFR) AF: 0.370 AC: 15348 AN: 41444

American (AMR) AF: 0.492 AC: 7511 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.513 AC: 1781 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1995 AN: 5164

South Asian (SAS) AF: 0.547 AC: 2631 AN: 4810

European-Finnish (FIN) AF: 0.506 AC: 5320 AN: 10516

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34479 AN: 67964

Other (OTH) AF: 0.454 AC: 959 AN: 2114

Alfa AF: 0.483 Hom.: 4120

Bravo AF: 0.457

Asia WGS AF: 0.444 AC: 1546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.9
DANN	Benign	0.36
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs1403937; hg19: chr7-57348122;