ENST00000717124.1:n.364+130181C>T

Variant names:

• chr15-97916486-G-A
• rs7163331
• ENST00000717124.1:n.364+130181C>T

Variant summary

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

The ENST00000717124.1(ENSG00000259199):​n.364+130181C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 152,138 control chromosomes in the GnomAD database, including 1,216 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 0.091 (1216 hom., cov: 32)
• Consequence: ENSG00000259199 ENST00000717124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 0 publications found

Genes affected

ENSG00000259199 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.228 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
ENSG00000259199	ENST00000717124.1	n.364+130181C>T		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13850 AN: 152020 Hom.: 1215 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0420

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.0572

Gnomad FIN AF: 0.0268

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.0685

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

GnomAD4 genome AF: 0.0912 AC: 13876 AN: 152138 Hom.: 1216 Cov.: 32 AF XY: 0.0879 AC XY: 6540 AN XY: 74366

African (AFR) AF: 0.232 AC: 9632 AN: 41474

American (AMR) AF: 0.0420 AC: 642 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3470

East Asian (EAS) AF: 0.00484 AC: 25 AN: 5170

South Asian (SAS) AF: 0.0570 AC: 275 AN: 4824

European-Finnish (FIN) AF: 0.0268 AC: 284 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0412 AC: 2802 AN: 68000

Other (OTH) AF: 0.0678 AC: 143 AN: 2110

Alfa AF: 0.0488 Hom.: 846

Bravo AF: 0.0986

Asia WGS AF: 0.0490 AC: 172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.4
DANN	Benign	0.70
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7163331; hg19: chr15-98459716;