rs9905258

Variant names:

• chr17-6003941-A-G
• rs9905258
• ENST00000573619.1:c.-289+13920A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000573619.1(ENSG00000285471):​c.-289+13920A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,038 control chromosomes in the GnomAD database, including 12,697 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 0.39 (12697 hom., cov: 32)
• Consequence: ENSG00000285471 ENST00000573619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.586

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 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
ENSG00000285471	ENST00000573619.1	c.-289+13920A>G		intron_variant	Intron 4 of 4	2		ENSP00000461865.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59841 AN: 151920 Hom.: 12694 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.394 AC: 59869 AN: 152038 Hom.: 12697 Cov.: 32 AF XY: 0.394 AC XY: 29307 AN XY: 74316

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.556

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.408

Alfa AF: 0.425 Hom.: 2383

Bravo AF: 0.389

Asia WGS AF: 0.534 AC: 1855 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	1.0
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9905258; hg19: chr17-5907261; COSMIC: COSV73818336;