6-165176932-G-T

Variant names:

• chr6-165176932-G-T
• rs9459317

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 0.235 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
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.404 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: 0.235 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

African (AFR) AF: 0.410 AC: 16976 AN: 41448

American (AMR) AF: 0.235 AC: 3585 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 473 AN: 3466

East Asian (EAS) AF: 0.226 AC: 1171 AN: 5172

South Asian (SAS) AF: 0.0962 AC: 464 AN: 4824

European-Finnish (FIN) AF: 0.142 AC: 1497 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.159 AC: 10808 AN: 67948

Other (OTH) AF: 0.228 AC: 480 AN: 2106

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
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9459317; hg19: chr6-165590421;