6-113926604-T-C

Variant names:

• chr6-113926604-T-C
• rs189512

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 0.682 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.753 AC: 29427 AN: 39098

American (AMR) AF: 0.630 AC: 9231 AN: 14660

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2358 AN: 3408

East Asian (EAS) AF: 0.714 AC: 3495 AN: 4896

South Asian (SAS) AF: 0.679 AC: 3120 AN: 4596

European-Finnish (FIN) AF: 0.637 AC: 5344 AN: 8390

Middle Eastern (MID) AF: 0.734 AC: 201 AN: 274

European-Non Finnish (NFE) AF: 0.654 AC: 43106 AN: 65898

Other (OTH) AF: 0.674 AC: 1357 AN: 2012

Alfa AF: 0.705 Hom.: 6215

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

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