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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.322 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

Gnomad4 AFR AF: 0.164

Gnomad4 AMR AF: 0.442

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.605

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.387

Gnomad4 NFE AF: 0.357

Gnomad4 OTH AF: 0.319

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2187968; hg19: chr1-167773438;