chr13-37601054-A-G

Variant names:

• chr13-37601054-A-G
• rs9547970
• ENST00000744989.1:n.48+4017A>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+4017A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,794 control chromosomes in the GnomAD database, including 12,398 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 0.40 (12398 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.436 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+4017A>G		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+4017A>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60893 AN: 151676 Hom.: 12377 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.402 AC: 60950 AN: 151794 Hom.: 12398 Cov.: 32 AF XY: 0.395 AC XY: 29314 AN XY: 74196

African (AFR) AF: 0.404 AC: 16731 AN: 41428

American (AMR) AF: 0.445 AC: 6767 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.555 AC: 1925 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1197 AN: 5160

South Asian (SAS) AF: 0.396 AC: 1915 AN: 4830

European-Finnish (FIN) AF: 0.330 AC: 3488 AN: 10566

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27635 AN: 67810

Other (OTH) AF: 0.421 AC: 888 AN: 2110

Alfa AF: 0.395 Hom.: 1530

Bravo AF: 0.410

Asia WGS AF: 0.326 AC: 1133 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs9547970; hg19: chr13-38175191;