13-105139456-G-T

Variant names:

• chr13-105139456-G-T
• rs4476030
• ENST00000746226.1:n.141+652C>A

Variant summary

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

The ENST00000746226.1(ENSG00000297213):​n.141+652C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,134 control chromosomes in the GnomAD database, including 4,877 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 0.24 (4877 hom., cov: 32)
• Consequence: ENSG00000297213 ENST00000746226.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 3 publications found

Genes affected

ENSG00000297213 (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 (EAS) allele frequency at 95% confidence interval = 0.486 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
ENSG00000297213	ENST00000746226.1	n.141+652C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36386 AN: 152016 Hom.: 4886 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.239 AC: 36371 AN: 152134 Hom.: 4877 Cov.: 32 AF XY: 0.242 AC XY: 17990 AN XY: 74366

African (AFR) AF: 0.142 AC: 5888 AN: 41524

American (AMR) AF: 0.199 AC: 3039 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2585 AN: 5148

South Asian (SAS) AF: 0.326 AC: 1572 AN: 4822

European-Finnish (FIN) AF: 0.267 AC: 2830 AN: 10590

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18618 AN: 67980

Other (OTH) AF: 0.238 AC: 502 AN: 2108

Alfa AF: 0.262 Hom.: 6880

Bravo AF: 0.235

Asia WGS AF: 0.351 AC: 1222 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	5.4
DANN	Benign	0.38
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs4476030; hg19: chr13-105791807;