rs1157146

Variant names:

• chr1-104909124-T-C
• rs1157146

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 0.651 in 151,776 control chromosomes in the GnomAD database, including 32,615 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 0.65 (32615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.707 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: 0.651 AC: 98727 AN: 151658 Hom.: 32591 Cov.: 32

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.651 AC: 98797 AN: 151776 Hom.: 32615 Cov.: 32 AF XY: 0.646 AC XY: 47862 AN XY: 74144

African (AFR) AF: 0.572 AC: 23704 AN: 41428

American (AMR) AF: 0.661 AC: 10044 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2288 AN: 3468

East Asian (EAS) AF: 0.418 AC: 2154 AN: 5158

South Asian (SAS) AF: 0.586 AC: 2821 AN: 4814

European-Finnish (FIN) AF: 0.687 AC: 7229 AN: 10526

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.713 AC: 48369 AN: 67870

Other (OTH) AF: 0.645 AC: 1358 AN: 2104

Alfa AF: 0.682 Hom.: 7466

Bravo AF: 0.641

Asia WGS AF: 0.537 AC: 1868 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.24
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1157146; hg19: chr1-105451746; COSMIC: COSV59983380;