ENST00000826415.1:n.97-1038A>T

Variant names:

• chr15-48812737-A-T
• rs7182710
• ENST00000826415.1:n.97-1038A>T

Variant summary

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

The ENST00000826415.1(ENSG00000259700):​n.97-1038A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,058 control chromosomes in the GnomAD database, including 13,463 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 0.41 (13463 hom., cov: 32)
• Consequence: ENSG00000259700 ENST00000826415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.61
• Publications: 3 publications found

Genes affected

ENSG00000259700 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259700	ENST00000826415.1	n.97-1038A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62697 AN: 151940 Hom.: 13461 Cov.: 32

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.412 AC: 62710 AN: 152058 Hom.: 13463 Cov.: 32 AF XY: 0.406 AC XY: 30151 AN XY: 74328

African (AFR) AF: 0.326 AC: 13499 AN: 41454

American (AMR) AF: 0.413 AC: 6307 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1921 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1712 AN: 5162

South Asian (SAS) AF: 0.370 AC: 1787 AN: 4824

European-Finnish (FIN) AF: 0.364 AC: 3844 AN: 10562

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 32033 AN: 67984

Other (OTH) AF: 0.456 AC: 964 AN: 2116

Alfa AF: 0.433 Hom.: 1844

Bravo AF: 0.415

Asia WGS AF: 0.294 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.68
PhyloP100		1.6

Splicing

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

Other links and lift over

dbSNP: rs7182710; hg19: chr15-49104934;