rs2201806

Positions:

• chr6-164561117-C-T

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 0.383 in 151,960 control chromosomes in the GnomAD database, including 11,713 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 0.38 (11713 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58204 AN: 151842 Hom.: 11703 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.505

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.383 AC: 58246 AN: 151960 Hom.: 11713 Cov.: 32 AF XY: 0.384 AC XY: 28537 AN XY: 74264

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.376

Alfa AF: 0.412 Hom.: 2079

Bravo AF: 0.390

Asia WGS AF: 0.432 AC: 1499 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2201806; hg19: chr6-164982150; COSMIC: COSV69432953;