rs617991

Variant names:

• chr3-21299371-T-C
• rs617991

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 0.4 in 151,882 control chromosomes in the GnomAD database, including 13,197 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 0.40 (13197 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.5 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: 0.400 AC: 60772 AN: 151764 Hom.: 13192 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.400 AC: 60802 AN: 151882 Hom.: 13197 Cov.: 31 AF XY: 0.395 AC XY: 29356 AN XY: 74240

African (AFR) AF: 0.282 AC: 11699 AN: 41428

American (AMR) AF: 0.319 AC: 4873 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3466

East Asian (EAS) AF: 0.136 AC: 701 AN: 5136

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4812

European-Finnish (FIN) AF: 0.468 AC: 4934 AN: 10532

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34251 AN: 67940

Other (OTH) AF: 0.416 AC: 877 AN: 2110

Alfa AF: 0.422 Hom.: 2065

Bravo AF: 0.383

Asia WGS AF: 0.201 AC: 699 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.7
DANN	Benign	0.88
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs617991; hg19: chr3-21340863;