rs1268161

Variant names:

• chr6-108690630-G-A
• rs1268161

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 0.221 in 152,228 control chromosomes in the GnomAD database, including 4,744 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 0.22 (4744 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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: 0.221 AC: 33582 AN: 152110 Hom.: 4733 Cov.: 32

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0985

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.221 AC: 33634 AN: 152228 Hom.: 4744 Cov.: 32 AF XY: 0.215 AC XY: 15987 AN XY: 74446

African (AFR) AF: 0.394 AC: 16342 AN: 41486

American (AMR) AF: 0.225 AC: 3438 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0985 AC: 342 AN: 3472

East Asian (EAS) AF: 0.0584 AC: 303 AN: 5188

South Asian (SAS) AF: 0.112 AC: 541 AN: 4828

European-Finnish (FIN) AF: 0.114 AC: 1210 AN: 10612

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10845 AN: 68026

Other (OTH) AF: 0.217 AC: 458 AN: 2114

Alfa AF: 0.223 Hom.: 708

Bravo AF: 0.240

Asia WGS AF: 0.126 AC: 440 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs1268161; hg19: chr6-109011833; COSMIC: COSV60264971;