rs17594362

Variant names:

• chr13-41565109-C-T
• rs17594362
• ENST00000674320.1:n.462+1631C>T

Variant summary

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

The ENST00000674320.1(ENSG00000288598):​n.462+1631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,166 control chromosomes in the GnomAD database, including 1,647 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 0.13 (1647 hom., cov: 33)
• Consequence: ENSG00000288598 ENST00000674320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 17 publications found

Genes affected

ENSG00000288598 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000674320.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288598	ENST00000674320.1		n.462+1631C>T		intron	N/A
	ENSG00000288598	ENST00000674416.1		n.1720+1631C>T		intron	N/A
	ENSG00000288598	ENST00000842280.1		n.588+6270C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19812 AN: 152046 Hom.: 1641 Cov.: 33

Gnomad AFR AF: 0.0428

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.228

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.130 AC: 19840 AN: 152166 Hom.: 1647 Cov.: 33 AF XY: 0.137 AC XY: 10201 AN XY: 74382

African (AFR) AF: 0.0430 AC: 1786 AN: 41546

American (AMR) AF: 0.239 AC: 3647 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 524 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1174 AN: 5172

South Asian (SAS) AF: 0.245 AC: 1180 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10568

Middle Eastern (MID) AF: 0.175 AC: 51 AN: 292

European-Non Finnish (NFE) AF: 0.133 AC: 9019 AN: 67990

Other (OTH) AF: 0.145 AC: 306 AN: 2112

Alfa AF: 0.133 Hom.: 4617

Bravo AF: 0.128

Asia WGS AF: 0.243 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs17594362; hg19: chr13-42139245;