6-160866301-C-T

Position:

• chr6-160866301-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 0.685 in 151,956 control chromosomes in the GnomAD database, including 35,926 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 0.69 (35926 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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: 0.685 AC: 103999 AN: 151838 Hom.: 35876 Cov.: 31

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.685 AC: 104106 AN: 151956 Hom.: 35926 Cov.: 31 AF XY: 0.690 AC XY: 51255 AN XY: 74254

Gnomad4 AFR AF: 0.635

Gnomad4 AMR AF: 0.745

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.676

Alfa AF: 0.678 Hom.: 17708

Bravo AF: 0.683

Asia WGS AF: 0.850 AC: 2954 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	0.25
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2465868; hg19: chr6-161287333; COSMIC: COSV69432121;