rs9479087

Variant names:

• chr6-151621879-C-T
• rs9479087

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 0.214 in 152,042 control chromosomes in the GnomAD database, including 3,625 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 0.21 (3625 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 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: 0.214 AC: 32439 AN: 151926 Hom.: 3616 Cov.: 31

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.0937

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.169

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.214 AC: 32484 AN: 152042 Hom.: 3625 Cov.: 31 AF XY: 0.212 AC XY: 15766 AN XY: 74312

African (AFR) AF: 0.279 AC: 11562 AN: 41430

American (AMR) AF: 0.155 AC: 2369 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 749 AN: 3468

East Asian (EAS) AF: 0.0939 AC: 487 AN: 5186

South Asian (SAS) AF: 0.168 AC: 809 AN: 4814

European-Finnish (FIN) AF: 0.272 AC: 2870 AN: 10560

Middle Eastern (MID) AF: 0.171 AC: 50 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13093 AN: 67976

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.194 Hom.: 9207

Bravo AF: 0.208

Asia WGS AF: 0.154 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.93
DANN	Benign	0.47
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs9479087; hg19: chr6-151943014;