6-160834512-C-T

Variant names:

• chr6-160834512-C-T
• rs1937479

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 0.626 in 151,670 control chromosomes in the GnomAD database, including 30,278 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 0.63 (30278 hom., cov: 32)
• Consequence: LOC107986665 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.768
• Publications: 5 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.626 AC: 94823 AN: 151552 Hom.: 30231 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.626 AC: 94930 AN: 151670 Hom.: 30278 Cov.: 32 AF XY: 0.633 AC XY: 46870 AN XY: 74094

African (AFR) AF: 0.672 AC: 27843 AN: 41446

American (AMR) AF: 0.713 AC: 10871 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1832 AN: 3452

East Asian (EAS) AF: 0.979 AC: 5077 AN: 5186

South Asian (SAS) AF: 0.717 AC: 3449 AN: 4812

European-Finnish (FIN) AF: 0.556 AC: 5842 AN: 10516

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38006 AN: 67706

Other (OTH) AF: 0.652 AC: 1373 AN: 2106

Alfa AF: 0.554 Hom.: 2547

Bravo AF: 0.638

Asia WGS AF: 0.839 AC: 2911 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.53
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1937479; hg19: chr6-161255544;