6-116939906-T-C

Variant names:

• chr6-116939906-T-C
• rs1741660

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 151,968 control chromosomes in the GnomAD database, including 44,310 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 (44310 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.802 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: 0.761 AC: 115505 AN: 151848 Hom.: 44293 Cov.: 30

Gnomad AFR AF: 0.735

Gnomad AMI AF: 0.887

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.815

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: 115575 AN: 151968 Hom.: 44310 Cov.: 30 AF XY: 0.750 AC XY: 55702 AN XY: 74272

African (AFR) AF: 0.734 AC: 30428 AN: 41428

American (AMR) AF: 0.741 AC: 11310 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2982 AN: 3470

East Asian (EAS) AF: 0.600 AC: 3100 AN: 5168

South Asian (SAS) AF: 0.582 AC: 2801 AN: 4812

European-Finnish (FIN) AF: 0.701 AC: 7386 AN: 10532

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

European-Non Finnish (NFE) AF: 0.807 AC: 54884 AN: 67974

Other (OTH) AF: 0.776 AC: 1636 AN: 2108

Alfa AF: 0.791 Hom.: 40786

Bravo AF: 0.769

Asia WGS AF: 0.581 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	17
DANN	Benign	0.80
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs1741660; hg19: chr6-117261069;