chr13-95387926-T-A

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.

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.148A>T		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000304941	ENST00000807275.1		n.160+16399A>T		intron	N/A
	ENSG00000304941	ENST00000807276.1		n.208+16260A>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs10508012;

hg19: chr13-96040180;