chr17-6003941-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000573619.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285471	ENST00000573619.1	TSL:2	c.-289+13920A>G		intron	N/A	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

African (AFR) AF: 0.227 AC: 9436 AN: 41502

American (AMR) AF: 0.431 AC: 6585 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3466

East Asian (EAS) AF: 0.556 AC: 2870 AN: 5164

South Asian (SAS) AF: 0.445 AC: 2140 AN: 4808

European-Finnish (FIN) AF: 0.440 AC: 4646 AN: 10562

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31445 AN: 67954

Other (OTH) AF: 0.408 AC: 860 AN: 2110

Alfa AF: 0.420 Hom.: 2403

Bravo AF: 0.389

Asia WGS AF: 0.534 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.21
PhyloP100		-0.59

Splicing

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

Other links and lift over

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