chr13-37611591-A-G

Variant names:

• chr13-37611591-A-G
• rs9547976
• ENST00000744989.1:n.48+14554A>G

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+14554A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 151,764 control chromosomes in the GnomAD database, including 3,713 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 0.20 (3713 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 2 publications found

Genes affected

ENSG00000297050 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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
ENSG00000297050	ENST00000744989.1	n.48+14554A>G		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+14554A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30453 AN: 151646 Hom.: 3714 Cov.: 32

Gnomad AFR AF: 0.0781

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0633

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.201 AC: 30455 AN: 151764 Hom.: 3713 Cov.: 32 AF XY: 0.200 AC XY: 14844 AN XY: 74112

African (AFR) AF: 0.0779 AC: 3228 AN: 41462

American (AMR) AF: 0.169 AC: 2579 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 737 AN: 3464

East Asian (EAS) AF: 0.0636 AC: 326 AN: 5122

South Asian (SAS) AF: 0.138 AC: 661 AN: 4806

European-Finnish (FIN) AF: 0.332 AC: 3461 AN: 10434

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18699 AN: 67924

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.220 Hom.: 547

Bravo AF: 0.183

Asia WGS AF: 0.145 AC: 507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.68
DANN	Benign	0.51
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs9547976; hg19: chr13-38185728;