chr13-37601702-T-C

Variant names:

• chr13-37601702-T-C
• rs17197936
• ENST00000744989.1:n.48+4665T>C

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+4665T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 152,084 control chromosomes in the GnomAD database, including 298 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 0.052 (298 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 3 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=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0742 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744989.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297050	ENST00000744989.1		n.48+4665T>C		intron	N/A
	ENSG00000297050	ENST00000744990.1		n.70+4665T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0521 AC: 7913 AN: 151966 Hom.: 297 Cov.: 32

Gnomad AFR AF: 0.0131

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0548

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0442

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0759

Gnomad OTH AF: 0.0723

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

GnomAD4 genome AF: 0.0520 AC: 7907 AN: 152084 Hom.: 298 Cov.: 32 AF XY: 0.0492 AC XY: 3662 AN XY: 74368

African (AFR) AF: 0.0130 AC: 540 AN: 41534

American (AMR) AF: 0.0547 AC: 832 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 626 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4822

European-Finnish (FIN) AF: 0.0442 AC: 469 AN: 10612

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0759 AC: 5155 AN: 67928

Other (OTH) AF: 0.0716 AC: 151 AN: 2110

Alfa AF: 0.0635 Hom.: 41

Bravo AF: 0.0529

Asia WGS AF: 0.00808 AC: 28 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.65
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs17197936; hg19: chr13-38175839;