rs2187968

Variant names:

• chr1-167804201-T-A
• rs2187968

Your query was ambiguous. Multiple possible variants found:

• chr1-167804201-T-A
• chr1-167804201-T-C

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 0.322 in 151,886 control chromosomes in the GnomAD database, including 8,848 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 0.32 (8848 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.545
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.587 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: 0.322 AC: 48848 AN: 151768 Hom.: 8839 Cov.: 30

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.605

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.387

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.357

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.322 AC: 48878 AN: 151886 Hom.: 8848 Cov.: 30 AF XY: 0.326 AC XY: 24208 AN XY: 74226

African (AFR) AF: 0.164 AC: 6787 AN: 41444

American (AMR) AF: 0.442 AC: 6741 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1073 AN: 3462

East Asian (EAS) AF: 0.605 AC: 3117 AN: 5154

South Asian (SAS) AF: 0.383 AC: 1843 AN: 4814

European-Finnish (FIN) AF: 0.387 AC: 4074 AN: 10532

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.357 AC: 24246 AN: 67914

Other (OTH) AF: 0.319 AC: 674 AN: 2114

Alfa AF: 0.335 Hom.: 1105

Bravo AF: 0.322

Asia WGS AF: 0.502 AC: 1743 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.49
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs2187968; hg19: chr1-167773438;