rs2985159

Variant names:

• chr13-37602352-T-G
• rs2985159
• ENST00000744989.1:n.48+5315T>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+5315T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,892 control chromosomes in the GnomAD database, including 6,989 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 0.29 (6989 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.474
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 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+5315T>G		intron_variant	Intron 1 of 4
ENSG00000297050	ENST00000744990.1	n.70+5315T>G		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44639 AN: 151774 Hom.: 6979 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44667 AN: 151892 Hom.: 6989 Cov.: 32 AF XY: 0.285 AC XY: 21189 AN XY: 74254

African (AFR) AF: 0.206 AC: 8552 AN: 41468

American (AMR) AF: 0.290 AC: 4419 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1707 AN: 3466

East Asian (EAS) AF: 0.162 AC: 835 AN: 5168

South Asian (SAS) AF: 0.334 AC: 1608 AN: 4816

European-Finnish (FIN) AF: 0.253 AC: 2679 AN: 10574

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23874 AN: 67868

Other (OTH) AF: 0.313 AC: 662 AN: 2112

Alfa AF: 0.339 Hom.: 4941

Bravo AF: 0.295

Asia WGS AF: 0.258 AC: 897 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	13
DANN	Benign	0.72
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs2985159; hg19: chr13-38176489; COSMIC: COSV65713182;