rs1268161

Variant names:

• chr6-108690630-G-A
• rs1268161

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 0.221 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.0985

Gnomad4 EAS AF: 0.0584

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.217

Alfa AF: 0.216 Hom.: 643

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

Splicing

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

Publications

LitVar

Other links and lift over

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