rs10508013

Variant names:

• chr13-95387778-G-A
• rs10508013
• ENST00000807278.1:n.296C>T

Variant summary

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

The ENST00000807278.1(ENSG00000304941):​n.296C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,858 control chromosomes in the GnomAD database, including 5,471 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 0.26 (5471 hom., cov: 31)
• Consequence: ENSG00000304941 ENST00000807278.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903193	XR_007063839.1	n.764+16547C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304941	ENST00000807278.1	n.296C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000304941	ENST00000807275.1	n.160+16547C>T		intron_variant	Intron 1 of 1
ENSG00000304941	ENST00000807276.1	n.208+16408C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39866 AN: 151740 Hom.: 5460 Cov.: 31

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.176

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.263 AC: 39894 AN: 151858 Hom.: 5471 Cov.: 31 AF XY: 0.263 AC XY: 19497 AN XY: 74192

African (AFR) AF: 0.317 AC: 13128 AN: 41392

American (AMR) AF: 0.201 AC: 3058 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 732 AN: 3468

East Asian (EAS) AF: 0.114 AC: 589 AN: 5166

South Asian (SAS) AF: 0.175 AC: 840 AN: 4810

European-Finnish (FIN) AF: 0.309 AC: 3248 AN: 10516

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17422 AN: 67966

Other (OTH) AF: 0.273 AC: 574 AN: 2106

Alfa AF: 0.268 Hom.: 719

Bravo AF: 0.253

Asia WGS AF: 0.175 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.3
DANN	Benign	0.49
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs10508013; hg19: chr13-96040032;