chr6-160834512-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986665		n.160834512C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;