rs2441701

Variant names:

• chr8-101157875-C-T
• rs2441701

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 0.655 in 152,074 control chromosomes in the GnomAD database, including 34,543 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 0.66 (34543 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99548 AN: 151956 Hom.: 34476 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.446

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.655 AC: 99677 AN: 152074 Hom.: 34543 Cov.: 32 AF XY: 0.654 AC XY: 48572 AN XY: 74302

African (AFR) AF: 0.893 AC: 37071 AN: 41516

American (AMR) AF: 0.660 AC: 10095 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3472

East Asian (EAS) AF: 0.445 AC: 2303 AN: 5170

South Asian (SAS) AF: 0.568 AC: 2733 AN: 4812

European-Finnish (FIN) AF: 0.585 AC: 6157 AN: 10524

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37696 AN: 67968

Other (OTH) AF: 0.608 AC: 1287 AN: 2116

Alfa AF: 0.575 Hom.: 43980

Bravo AF: 0.671

Asia WGS AF: 0.558 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.36
DANN	Benign	0.65
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2441701; hg19: chr8-102170103;