6-92851432-C-T

Variant names:

• chr6-92851432-C-T
• rs1040155

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 0.7 in 152,020 control chromosomes in the GnomAD database, including 37,671 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 0.70 (37671 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.837 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: 0.700 AC: 106381 AN: 151904 Hom.: 37638 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.858

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.700 AC: 106461 AN: 152020 Hom.: 37671 Cov.: 32 AF XY: 0.705 AC XY: 52339 AN XY: 74264

African (AFR) AF: 0.594 AC: 24636 AN: 41464

American (AMR) AF: 0.749 AC: 11427 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2612 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4424 AN: 5158

South Asian (SAS) AF: 0.825 AC: 3981 AN: 4824

European-Finnish (FIN) AF: 0.744 AC: 7851 AN: 10552

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49264 AN: 67970

Other (OTH) AF: 0.667 AC: 1408 AN: 2110

Alfa AF: 0.723 Hom.: 177839

Bravo AF: 0.695

Asia WGS AF: 0.804 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.54
DANN	Benign	0.73
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1040155; hg19: chr6-93561150; COSMIC: COSV69413584;