rs2171981

Variant names:

• chr6-168125560-T-C
• rs2171981

Your query was ambiguous. Multiple possible variants found:

• chr6-168125560-T-C
• chr6-168125560-T-G

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 0.444 in 151,964 control chromosomes in the GnomAD database, including 16,057 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 0.44 (16057 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.613 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: 0.444 AC: 67427 AN: 151846 Hom.: 16041 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.444 AC: 67498 AN: 151964 Hom.: 16057 Cov.: 32 AF XY: 0.438 AC XY: 32563 AN XY: 74274

African (AFR) AF: 0.619 AC: 25673 AN: 41462

American (AMR) AF: 0.347 AC: 5295 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3466

East Asian (EAS) AF: 0.139 AC: 712 AN: 5132

South Asian (SAS) AF: 0.298 AC: 1435 AN: 4816

European-Finnish (FIN) AF: 0.419 AC: 4435 AN: 10576

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27473 AN: 67924

Other (OTH) AF: 0.384 AC: 811 AN: 2114

Alfa AF: 0.388 Hom.: 17861

Bravo AF: 0.447

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.38
DANN	Benign	0.31
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2171981; hg19: chr6-168526240; COSMIC: COSV60303396;