6-79397962-C-T

Variant names:

• chr6-79397962-C-T
• rs17743190

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 0.0843 in 152,192 control chromosomes in the GnomAD database, including 599 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 0.084 (599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 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: 0.0844 AC: 12835 AN: 152074 Hom.: 599 Cov.: 32

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0518

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0843 AC: 12832 AN: 152192 Hom.: 599 Cov.: 32 AF XY: 0.0826 AC XY: 6148 AN XY: 74404

African (AFR) AF: 0.0411 AC: 1708 AN: 41530

American (AMR) AF: 0.0907 AC: 1387 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 570 AN: 3470

East Asian (EAS) AF: 0.101 AC: 521 AN: 5172

South Asian (SAS) AF: 0.127 AC: 611 AN: 4818

European-Finnish (FIN) AF: 0.0518 AC: 548 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7215 AN: 68000

Other (OTH) AF: 0.107 AC: 227 AN: 2114

Alfa AF: 0.101 Hom.: 1006

Bravo AF: 0.0849

Asia WGS AF: 0.109 AC: 380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.48
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs17743190; hg19: chr6-80107679;