6-32702178-G-T

Variant names:

• chr6-32702178-G-T
• rs9275406

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 0.295 in 151,766 control chromosomes in the GnomAD database, including 7,100 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 0.29 (7100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.542
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 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: 0.294 AC: 44637 AN: 151648 Hom.: 7084 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.295 AC: 44698 AN: 151766 Hom.: 7100 Cov.: 32 AF XY: 0.304 AC XY: 22564 AN XY: 74170

African (AFR) AF: 0.294 AC: 12165 AN: 41392

American (AMR) AF: 0.396 AC: 6035 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1122 AN: 3454

East Asian (EAS) AF: 0.296 AC: 1527 AN: 5166

South Asian (SAS) AF: 0.211 AC: 1013 AN: 4808

European-Finnish (FIN) AF: 0.466 AC: 4917 AN: 10546

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.249 AC: 16891 AN: 67858

Other (OTH) AF: 0.287 AC: 603 AN: 2104

Alfa AF: 0.281 Hom.: 6806

Bravo AF: 0.295

Asia WGS AF: 0.277 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
DANN	Benign	0.80
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs9275406; hg19: chr6-32669955;