6-116939906-T-C

Variant names:

• chr6-116939906-T-C
• rs1741660

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.859

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.582

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.807

Gnomad4 OTH AF: 0.776

Alfa AF: 0.785 Hom.: 28326

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1741660; hg19: chr6-117261069;