rs601962

Variant names:

• chr8-29393029-T-C
• rs601962

Your query was ambiguous. Multiple possible variants found:

• chr8-29393029-T-C
• chr8-29393029-T-G

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 0.548 in 151,890 control chromosomes in the GnomAD database, including 25,054 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 0.55 (25054 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 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: 0.548 AC: 83127 AN: 151772 Hom.: 25045 Cov.: 30

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.548 AC: 83170 AN: 151890 Hom.: 25054 Cov.: 30 AF XY: 0.543 AC XY: 40287 AN XY: 74212

African (AFR) AF: 0.312 AC: 12904 AN: 41404

American (AMR) AF: 0.501 AC: 7646 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2229 AN: 3466

East Asian (EAS) AF: 0.321 AC: 1659 AN: 5176

South Asian (SAS) AF: 0.541 AC: 2600 AN: 4802

European-Finnish (FIN) AF: 0.634 AC: 6666 AN: 10514

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47532 AN: 67952

Other (OTH) AF: 0.584 AC: 1232 AN: 2110

Alfa AF: 0.647 Hom.: 55286

Bravo AF: 0.525

Asia WGS AF: 0.413 AC: 1435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.44
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs601962; hg19: chr8-29250546;