rs9479482

Variant names:

• chr6-150036876-T-C
• rs9479482

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 0.357 in 152,132 control chromosomes in the GnomAD database, including 10,511 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 0.36 (10511 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.478
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.441 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: 0.357 AC: 54257 AN: 152014 Hom.: 10516 Cov.: 33

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.357 AC: 54251 AN: 152132 Hom.: 10511 Cov.: 33 AF XY: 0.354 AC XY: 26356 AN XY: 74350

African (AFR) AF: 0.219 AC: 9094 AN: 41516

American (AMR) AF: 0.310 AC: 4736 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1182 AN: 5174

South Asian (SAS) AF: 0.379 AC: 1830 AN: 4826

European-Finnish (FIN) AF: 0.424 AC: 4473 AN: 10556

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30264 AN: 67980

Other (OTH) AF: 0.359 AC: 759 AN: 2112

Alfa AF: 0.414 Hom.: 60215

Bravo AF: 0.339

Asia WGS AF: 0.289 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.7
DANN	Benign	0.47
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs9479482; hg19: chr6-150358012;