chr6-113344125-C-T

Variant names:

• chr6-113344125-C-T
• rs7765175

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 0.305 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.305 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

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.373

Gnomad4 OTH AF: 0.328

Alfa AF: 0.366 Hom.: 14207

Bravo AF: 0.304

Asia WGS AF: 0.303 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7765175; hg19: chr6-113665327;