6-165176932-G-T

Position:

• chr6-165176932-G-T

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 0.235 in 152,020 control chromosomes in the GnomAD database, including 5,173 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 0.23 (5173 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.346

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 (AFR) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35628 AN: 151904 Hom.: 5157 Cov.: 33

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.0967

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.235 AC: 35683 AN: 152020 Hom.: 5173 Cov.: 33 AF XY: 0.232 AC XY: 17273 AN XY: 74324

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.0962

Gnomad4 FIN AF: 0.142

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.228

Alfa AF: 0.211 Hom.: 678

Bravo AF: 0.250

Asia WGS AF: 0.173 AC: 598 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	2.5
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9459317; hg19: chr6-165590421;