rs10508012

Variant names:

• chr13-95387926-T-A
• rs10508012
• ENST00000807278.1:n.148A>T

Variant summary

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

The ENST00000807278.1(ENSG00000304941):​n.148A>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 0.262 in 152,120 control chromosomes in the GnomAD database, including 5,458 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 (5458 hom., cov: 33)
• Consequence: ENSG00000304941 ENST00000807278.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830
• 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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903193	XR_007063839.1	n.764+16399A>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304941	ENST00000807278.1	n.148A>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000304941	ENST00000807275.1	n.160+16399A>T		intron_variant	Intron 1 of 1
ENSG00000304941	ENST00000807276.1	n.208+16260A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.262 AC: 39854 AN: 152002 Hom.: 5451 Cov.: 33

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.262 AC: 39874 AN: 152120 Hom.: 5458 Cov.: 33 AF XY: 0.262 AC XY: 19502 AN XY: 74360

African (AFR) AF: 0.315 AC: 13069 AN: 41498

American (AMR) AF: 0.201 AC: 3066 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 733 AN: 3470

East Asian (EAS) AF: 0.114 AC: 588 AN: 5178

South Asian (SAS) AF: 0.175 AC: 843 AN: 4830

European-Finnish (FIN) AF: 0.309 AC: 3265 AN: 10554

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

European-Non Finnish (NFE) AF: 0.257 AC: 17439 AN: 67984

Other (OTH) AF: 0.269 AC: 568 AN: 2112

Alfa AF: 0.266 Hom.: 675

Bravo AF: 0.253

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.3
DANN	Benign	0.65
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs10508012; hg19: chr13-96040180;