rs9293494

Positions:

• chr5-87908304-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287862 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287862	ENST00000655360.1	n.388-40428A>C		intron_variant
ENSG00000287862	ENST00000668454.1	n.219-40425A>C		intron_variant

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

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.0122

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.331

Alfa AF: 0.300 Hom.: 1352

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9293494; hg19: chr5-87204121;