rs7624691

Positions:

• chr3-137144237-T-C
• chr3-137144237-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.491 in 152,072 control chromosomes in the GnomAD database, including 18,789 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 0.49 (18789 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74577 AN: 151954 Hom.: 18769 Cov.: 32

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.428

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.491 AC: 74642 AN: 152072 Hom.: 18789 Cov.: 32 AF XY: 0.494 AC XY: 36732 AN XY: 74344

Gnomad4 AFR AF: 0.588

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.562

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.451

Gnomad4 NFE AF: 0.428

Gnomad4 OTH AF: 0.510

Alfa AF: 0.439 Hom.: 29564

Bravo AF: 0.498

Asia WGS AF: 0.560 AC: 1944 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.032
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7624691; hg19: chr3-136863079;