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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807278.1. 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	ENST00000807278.1		n.296C>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000304941	ENST00000807275.1		n.160+16547C>T		intron	N/A
	ENSG00000304941	ENST00000807276.1		n.208+16408C>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs10508013;

hg19: chr13-96040032;