6-160866301-C-T

Variant names:

• chr6-160866301-C-T
• rs2465868

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 0.685 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: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 6 publications found

Genes affected

LOC107986665 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.635 AC: 26295 AN: 41404

American (AMR) AF: 0.745 AC: 11385 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2021 AN: 3466

East Asian (EAS) AF: 0.979 AC: 5071 AN: 5178

South Asian (SAS) AF: 0.759 AC: 3640 AN: 4796

European-Finnish (FIN) AF: 0.721 AC: 7614 AN: 10558

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.676 AC: 45912 AN: 67950

Other (OTH) AF: 0.676 AC: 1430 AN: 2116

Alfa AF: 0.681 Hom.: 33556

Bravo AF: 0.683

Asia WGS AF: 0.850 AC: 2954 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.20
PhyloP100		-0.85

Splicing

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

Other links and lift over

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