rs951095

Variant names:

• chr13-104826293-C-T
• rs951095
• ENST00000807560.1:n.287-2506G>A

Variant summary

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

The ENST00000807560.1(ENSG00000304988):​n.287-2506G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 151,906 control chromosomes in the GnomAD database, including 11,588 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 0.38 (11588 hom., cov: 31)
• Consequence: ENSG00000304988 ENST00000807560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 9 publications found

Genes affected

ENSG00000304988 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807560.1. 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
	ENSG00000304988	ENST00000807560.1		n.287-2506G>A		intron	N/A
	ENSG00000304988	ENST00000807561.1		n.238+10910G>A		intron	N/A
	ENSG00000305002	ENST00000807621.1		n.173+2814C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58374 AN: 151788 Hom.: 11591 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.384 AC: 58393 AN: 151906 Hom.: 11588 Cov.: 31 AF XY: 0.397 AC XY: 29462 AN XY: 74204

African (AFR) AF: 0.385 AC: 15934 AN: 41420

American (AMR) AF: 0.471 AC: 7188 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 858 AN: 3468

East Asian (EAS) AF: 0.412 AC: 2116 AN: 5136

South Asian (SAS) AF: 0.418 AC: 2007 AN: 4802

European-Finnish (FIN) AF: 0.522 AC: 5510 AN: 10560

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23614 AN: 67952

Other (OTH) AF: 0.340 AC: 716 AN: 2106

Alfa AF: 0.352 Hom.: 41427

Bravo AF: 0.379

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.63
PhyloP100		-0.053

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: rs951095;

hg19: chr13-105478644;