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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984606	XR_001749993.2	n.297-2506G>A		intron_variant	Intron 2 of 3
LOC107984606	XR_001749994.2	n.296+10910G>A		intron_variant	Intron 2 of 2
LOC107984606	XR_001749995.2	n.296+10910G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304988	ENST00000807560.1	n.287-2506G>A		intron_variant	Intron 2 of 3
ENSG00000304988	ENST00000807561.1	n.238+10910G>A		intron_variant	Intron 2 of 2
ENSG00000305002	ENST00000807621.1	n.173+2814C>T		intron_variant	Intron 1 of 2
ENSG00000305002	ENST00000807622.1	n.156-2762C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs951095; hg19: chr13-105478644;