13-42701010-T-C

Variant names:

• chr13-42701010-T-C
• rs6561072
• ENST00000799325.1:n.506+19541A>G

Variant summary

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

The ENST00000799325.1(ENSG00000304062):​n.506+19541A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,106 control chromosomes in the GnomAD database, including 21,337 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 0.51 (21337 hom., cov: 33)
• Consequence: ENSG00000304062 ENST00000799325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527
• Publications: 6 publications found

Genes affected

ENSG00000304062 (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 (AFR) allele frequency at 95% confidence interval = 0.693 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
ENSG00000304062	ENST00000799325.1	n.506+19541A>G		intron_variant	Intron 2 of 3
ENSG00000304076	ENST00000799486.1	n.161+6628T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78070 AN: 151988 Hom.: 21304 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.514 AC: 78148 AN: 152106 Hom.: 21337 Cov.: 33 AF XY: 0.516 AC XY: 38385 AN XY: 74350

African (AFR) AF: 0.700 AC: 29031 AN: 41486

American (AMR) AF: 0.588 AC: 8992 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3468

East Asian (EAS) AF: 0.374 AC: 1936 AN: 5178

South Asian (SAS) AF: 0.380 AC: 1836 AN: 4830

European-Finnish (FIN) AF: 0.514 AC: 5429 AN: 10572

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27892 AN: 67980

Other (OTH) AF: 0.493 AC: 1040 AN: 2108

Alfa AF: 0.420 Hom.: 7576

Bravo AF: 0.530

Asia WGS AF: 0.410 AC: 1427 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	0.26
DANN	Benign	0.79
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6561072; hg19: chr13-43275146; COSMIC: COSV69348122;