rs17446593

Variant names:

• chr13-40553948-A-G
• rs17446593
• ENST00000636651.2:n.1459+5561T>C

Variant summary

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

The ENST00000636651.2(ENSG00000288542):​n.1459+5561T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,100 control chromosomes in the GnomAD database, including 2,738 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 0.19 (2738 hom., cov: 32)
• Consequence: ENSG00000288542 ENST00000636651.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730
• Publications: 20 publications found

Genes affected

ENSG00000288542 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.302 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
ENSG00000288542	ENST00000636651.2	n.1459+5561T>C		intron_variant	Intron 2 of 3	5

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28206 AN: 151982 Hom.: 2737 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.186 AC: 28217 AN: 152100 Hom.: 2738 Cov.: 32 AF XY: 0.190 AC XY: 14145 AN XY: 74342

African (AFR) AF: 0.178 AC: 7391 AN: 41484

American (AMR) AF: 0.218 AC: 3339 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3472

East Asian (EAS) AF: 0.127 AC: 657 AN: 5166

South Asian (SAS) AF: 0.315 AC: 1516 AN: 4808

European-Finnish (FIN) AF: 0.200 AC: 2114 AN: 10578

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12241 AN: 67994

Other (OTH) AF: 0.171 AC: 359 AN: 2102

Alfa AF: 0.181 Hom.: 4573

Bravo AF: 0.183

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		0.073

Splicing

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

Other links and lift over

dbSNP: rs17446593; hg19: chr13-41128085;