chr6-116939793-T-C

Variant names:

• chr6-116939793-T-C
• rs1741662

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 0.761 in 152,066 control chromosomes in the GnomAD database, including 44,336 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 0.76 (44336 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.777
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 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: 0.761 AC: 115579 AN: 151948 Hom.: 44320 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.583

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.816

Gnomad NFE AF: 0.807

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.761 AC: 115647 AN: 152066 Hom.: 44336 Cov.: 32 AF XY: 0.750 AC XY: 55740 AN XY: 74310

African (AFR) AF: 0.734 AC: 30453 AN: 41466

American (AMR) AF: 0.741 AC: 11312 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2983 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3089 AN: 5142

South Asian (SAS) AF: 0.583 AC: 2811 AN: 4820

European-Finnish (FIN) AF: 0.701 AC: 7410 AN: 10566

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.807 AC: 54902 AN: 68008

Other (OTH) AF: 0.776 AC: 1637 AN: 2110

Alfa AF: 0.797 Hom.: 21005

Bravo AF: 0.769

Asia WGS AF: 0.582 AC: 2027 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.57
DANN	Benign	0.58
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs1741662; hg19: chr6-117260956;