13-95351409-C-T

Variant names:

• chr13-95351409-C-T
• rs9516572
• ENST00000807275.1:n.*11G>A

Variant summary

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

The ENST00000807275.1(ENSG00000304941):​n.*11G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.477 in 151,472 control chromosomes in the GnomAD database, including 19,041 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 0.48 (19041 hom., cov: 31)
• Consequence: ENSG00000304941 ENST00000807275.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 4 publications found

Genes affected

ENSG00000304941 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903193	XR_007063839.1	n.*13G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304941	ENST00000807275.1	n.*11G>A		downstream_gene_variant
ENSG00000304941	ENST00000807276.1	n.*13G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.477 AC: 72227 AN: 151354 Hom.: 19049 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.483

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.477 AC: 72229 AN: 151472 Hom.: 19041 Cov.: 31 AF XY: 0.473 AC XY: 34967 AN XY: 73964

African (AFR) AF: 0.235 AC: 9710 AN: 41294

American (AMR) AF: 0.578 AC: 8795 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2038 AN: 3468

East Asian (EAS) AF: 0.467 AC: 2398 AN: 5138

South Asian (SAS) AF: 0.405 AC: 1933 AN: 4768

European-Finnish (FIN) AF: 0.496 AC: 5151 AN: 10386

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.597 AC: 40535 AN: 67906

Other (OTH) AF: 0.507 AC: 1067 AN: 2104

Alfa AF: 0.539 Hom.: 9447

Bravo AF: 0.478

Asia WGS AF: 0.449 AC: 1562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	4.8
DANN	Benign	0.90
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9516572; hg19: chr13-96003663;