rs11617518

Variant names:

• chr13-23716128-C-T
• rs11617518
• ENST00000691844.3:n.224-329C>T

Variant summary

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

The ENST00000691844.3(ENSG00000289332):​n.224-329C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 152,040 control chromosomes in the GnomAD database, including 21,583 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 0.50 (21583 hom., cov: 32)
• Consequence: ENSG00000289332 ENST00000691844.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 4 publications found

Genes affected

ENSG00000289332 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.687 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
ENSG00000289332	ENST00000691844.3	n.224-329C>T		intron_variant	Intron 1 of 2
ENSG00000289332	ENST00000848854.1	n.125-329C>T		intron_variant	Intron 1 of 2
ENSG00000289332	ENST00000848855.1	n.183-329C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75392 AN: 151922 Hom.: 21580 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.496 AC: 75411 AN: 152040 Hom.: 21583 Cov.: 32 AF XY: 0.498 AC XY: 36986 AN XY: 74300

African (AFR) AF: 0.204 AC: 8446 AN: 41468

American (AMR) AF: 0.606 AC: 9263 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1597 AN: 5158

South Asian (SAS) AF: 0.706 AC: 3406 AN: 4822

European-Finnish (FIN) AF: 0.557 AC: 5884 AN: 10562

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.631 AC: 42904 AN: 67956

Other (OTH) AF: 0.515 AC: 1086 AN: 2110

Alfa AF: 0.590 Hom.: 34047

Bravo AF: 0.479

Asia WGS AF: 0.541 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.58
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs11617518; hg19: chr13-24290267;