6-113344125-C-T

Variant names:

• chr6-113344125-C-T
• rs7765175

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 0.305 in 151,850 control chromosomes in the GnomAD database, including 7,961 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 0.30 (7961 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.489
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46275 AN: 151728 Hom.: 7958 Cov.: 31

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.305 AC: 46299 AN: 151850 Hom.: 7961 Cov.: 31 AF XY: 0.305 AC XY: 22648 AN XY: 74200

African (AFR) AF: 0.139 AC: 5748 AN: 41436

American (AMR) AF: 0.420 AC: 6400 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3466

East Asian (EAS) AF: 0.216 AC: 1114 AN: 5148

South Asian (SAS) AF: 0.385 AC: 1855 AN: 4814

European-Finnish (FIN) AF: 0.328 AC: 3459 AN: 10550

Middle Eastern (MID) AF: 0.432 AC: 126 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25319 AN: 67908

Other (OTH) AF: 0.328 AC: 690 AN: 2104

Alfa AF: 0.359 Hom.: 17423

Bravo AF: 0.304

Asia WGS AF: 0.303 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.67
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs7765175; hg19: chr6-113665327;