rs601962

Positions:

• chr8-29393029-T-C
• chr8-29393029-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 0.548 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.501

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.541

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.584

Alfa AF: 0.659 Hom.: 45202

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs601962; hg19: chr8-29250546;