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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.384

Alfa AF: 0.382 Hom.: 14513

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

Splicing

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

Publications

LitVar

Other links and lift over

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