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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807275.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304941	ENST00000807275.1		n.*11G>A		downstream_gene	N/A
	ENSG00000304941	ENST00000807276.1		n.*13G>A		downstream_gene	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9516572;

hg19: chr13-96003663;