6-113926604-T-C

Variant names:

• chr6-113926604-T-C
• rs189512

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 0.682 in 144,130 control chromosomes in the GnomAD database, including 33,368 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 0.68 (33368 hom., cov: 24)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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: 0.682 AC: 98279 AN: 144084 Hom.: 33351 Cov.: 24

Gnomad AFR AF: 0.753

Gnomad AMI AF: 0.749

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.682 AC: 98312 AN: 144130 Hom.: 33368 Cov.: 24 AF XY: 0.682 AC XY: 47663 AN XY: 69914

Gnomad4 AFR AF: 0.753

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.674

Alfa AF: 0.663 Hom.: 2603

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs189512; hg19: chr6-114247768; COSMIC: COSV58756838;