6-11617934-T-C

Position:

• chr6-11617934-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 0.504 in 151,740 control chromosomes in the GnomAD database, including 19,467 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 0.50 (19467 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76389 AN: 151628 Hom.: 19459 Cov.: 30

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.504 AC: 76440 AN: 151740 Hom.: 19467 Cov.: 30 AF XY: 0.506 AC XY: 37547 AN XY: 74134

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.503

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.483

Alfa AF: 0.455 Hom.: 18117

Bravo AF: 0.510

Asia WGS AF: 0.556 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.050
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs479526; hg19: chr6-11618167;