rs9387454

Variant names:

• chr6-117215621-C-T
• rs9387454

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 0.33 in 151,826 control chromosomes in the GnomAD database, including 9,803 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 0.33 (9803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.696 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: 0.330 AC: 50043 AN: 151710 Hom.: 9790 Cov.: 31

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.330 AC: 50080 AN: 151826 Hom.: 9803 Cov.: 31 AF XY: 0.339 AC XY: 25161 AN XY: 74144

African (AFR) AF: 0.129 AC: 5365 AN: 41448

American (AMR) AF: 0.477 AC: 7273 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1057 AN: 3466

East Asian (EAS) AF: 0.715 AC: 3645 AN: 5096

South Asian (SAS) AF: 0.417 AC: 2011 AN: 4822

European-Finnish (FIN) AF: 0.466 AC: 4880 AN: 10482

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24698 AN: 67954

Other (OTH) AF: 0.346 AC: 730 AN: 2108

Alfa AF: 0.360 Hom.: 1767

Bravo AF: 0.327

Asia WGS AF: 0.530 AC: 1840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.99
DANN	Benign	0.21
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9387454; hg19: chr6-117536784;