6-116939906-T-C

Position:

• chr6-116939906-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.116939906T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;