rs7990962

Variant names:

• chr13-42825109-A-G
• rs7990962

Your query was ambiguous. Multiple possible variants found:

• chr13-42825109-A-G
• chr13-42825109-A-T

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 0.202 in 152,166 control chromosomes in the GnomAD database, including 3,262 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 0.20 (3262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.326
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 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: 0.202 AC: 30768 AN: 152048 Hom.: 3258 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.187

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.202 AC: 30790 AN: 152166 Hom.: 3262 Cov.: 32 AF XY: 0.208 AC XY: 15497 AN XY: 74392

African (AFR) AF: 0.187 AC: 7784 AN: 41534

American (AMR) AF: 0.213 AC: 3250 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1668 AN: 5162

South Asian (SAS) AF: 0.293 AC: 1410 AN: 4818

European-Finnish (FIN) AF: 0.264 AC: 2795 AN: 10596

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.187 AC: 12696 AN: 67982

Other (OTH) AF: 0.190 AC: 403 AN: 2116

Alfa AF: 0.190 Hom.: 12646

Bravo AF: 0.199

Asia WGS AF: 0.288 AC: 1002 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.65
DANN	Benign	0.63
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs7990962; hg19: chr13-43399245;