15-97975562-C-G

Variant names:

• chr15-97975562-C-G
• rs4965121
• ENST00000717124.1:n.364+71105G>C

Variant summary

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

The ENST00000717124.1(ENSG00000259199):​n.364+71105G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,022 control chromosomes in the GnomAD database, including 23,562 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 0.53 (23562 hom., cov: 33)
• Consequence: ENSG00000259199 ENST00000717124.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 19 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.865 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+71105G>C		intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81190 AN: 151904 Hom.: 23555 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.596

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.886

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.534 AC: 81223 AN: 152022 Hom.: 23562 Cov.: 33 AF XY: 0.537 AC XY: 39896 AN XY: 74308

African (AFR) AF: 0.301 AC: 12486 AN: 41464

American (AMR) AF: 0.574 AC: 8761 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2291 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4590 AN: 5176

South Asian (SAS) AF: 0.750 AC: 3616 AN: 4824

European-Finnish (FIN) AF: 0.509 AC: 5366 AN: 10542

Middle Eastern (MID) AF: 0.548 AC: 160 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42226 AN: 67970

Other (OTH) AF: 0.562 AC: 1185 AN: 2110

Alfa AF: 0.430 Hom.: 1288

Bravo AF: 0.526

Asia WGS AF: 0.764 AC: 2655 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.51
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs4965121; hg19: chr15-98518792;