chr13-98086511-C-A

Variant names:

• chr13-98086511-C-A
• rs285070
• ENST00000717002.1:n.117-7348G>T

Variant summary

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

The ENST00000717002.1(ENSG00000293659):​n.117-7348G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 150,950 control chromosomes in the GnomAD database, including 47,748 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 0.76 (47748 hom., cov: 30)
• Consequence: ENSG00000293659 ENST00000717002.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 1 publications found

Genes affected

ENSG00000293659 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.95 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370328	XR_931670.4	n.73-19465G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293659	ENST00000717002.1	n.117-7348G>T		intron_variant	Intron 1 of 4
ENSG00000293659	ENST00000717003.1	n.91-7348G>T		intron_variant	Intron 1 of 4
ENSG00000293659	ENST00000717004.1	n.52-10701G>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.759 AC: 114456 AN: 150868 Hom.: 47759 Cov.: 30

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.793

Gnomad FIN AF: 0.932

Gnomad MID AF: 0.814

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.758 AC: 114462 AN: 150950 Hom.: 47748 Cov.: 30 AF XY: 0.755 AC XY: 55701 AN XY: 73748

African (AFR) AF: 0.410 AC: 16763 AN: 40918

American (AMR) AF: 0.720 AC: 10934 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3184 AN: 3470

East Asian (EAS) AF: 0.497 AC: 2560 AN: 5148

South Asian (SAS) AF: 0.792 AC: 3812 AN: 4812

European-Finnish (FIN) AF: 0.932 AC: 9525 AN: 10218

Middle Eastern (MID) AF: 0.804 AC: 230 AN: 286

European-Non Finnish (NFE) AF: 0.956 AC: 64946 AN: 67910

Other (OTH) AF: 0.785 AC: 1642 AN: 2092

Alfa AF: 0.872 Hom.: 12224

Bravo AF: 0.724

Asia WGS AF: 0.625 AC: 2166 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.2
DANN	Benign	0.74
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs285070; hg19: chr13-98738765;