rs9293494

Variant names:

• chr5-87908304-T-G
• rs9293494
• ENST00000655360.1:n.388-40428A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655360.1(ENSG00000287862):​n.388-40428A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 151,816 control chromosomes in the GnomAD database, including 11,407 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 0.34 (11407 hom., cov: 32)
• Consequence: ENSG00000287862 ENST00000655360.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0260
• Publications: 2 publications found

Genes affected

ENSG00000287862 (HGNC:):

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 = 0.621 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
ENSG00000287862	ENST00000655360.1	n.388-40428A>C		intron_variant	Intron 2 of 2
ENSG00000287862	ENST00000668454.1	n.219-40425A>C		intron_variant	Intron 2 of 3
ENSG00000287862	ENST00000815243.1	n.209-40425A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51701 AN: 151698 Hom.: 11378 Cov.: 32

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.341 AC: 51782 AN: 151816 Hom.: 11407 Cov.: 32 AF XY: 0.333 AC XY: 24709 AN XY: 74204

African (AFR) AF: 0.627 AC: 25970 AN: 41406

American (AMR) AF: 0.273 AC: 4160 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3468

East Asian (EAS) AF: 0.0122 AC: 63 AN: 5180

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4830

European-Finnish (FIN) AF: 0.137 AC: 1454 AN: 10604

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.244 AC: 16520 AN: 67792

Other (OTH) AF: 0.331 AC: 698 AN: 2110

Alfa AF: 0.310 Hom.: 1506

Bravo AF: 0.360

Asia WGS AF: 0.188 AC: 653 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.60
PhyloP100		0.026

Splicing

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

Other links and lift over

dbSNP: rs9293494; hg19: chr5-87204121;