chr15-47917521-C-T

Variant names:

• chr15-47917521-C-T
• rs16960341
• ENST00000560900.1:n.195+33017C>T

Variant summary

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

The ENST00000560900.1(ENSG00000259754):​n.195+33017C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0313 in 151,944 control chromosomes in the GnomAD database, including 211 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 0.031 (211 hom., cov: 31)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.169
• Publications: 1 publications found

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+33017C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.142+33017C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.82+2159C>T		intron_variant	Intron 1 of 2
LOC124900354	XR_007064618.1	n.143-31835C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+33017C>T		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-75188C>T		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-75188C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0314 AC: 4761 AN: 151824 Hom.: 211 Cov.: 31

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0376

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0664

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0253

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

GnomAD4 genome AF: 0.0313 AC: 4760 AN: 151944 Hom.: 211 Cov.: 31 AF XY: 0.0337 AC XY: 2502 AN XY: 74234

African (AFR) AF: 0.0324 AC: 1345 AN: 41484

American (AMR) AF: 0.0376 AC: 573 AN: 15258

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

East Asian (EAS) AF: 0.195 AC: 979 AN: 5016

South Asian (SAS) AF: 0.0660 AC: 318 AN: 4818

European-Finnish (FIN) AF: 0.0331 AC: 350 AN: 10582

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1070 AN: 67996

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0211 Hom.: 53

Bravo AF: 0.0324

Asia WGS AF: 0.0970 AC: 336 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.52
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs16960341; hg19: chr15-48209718;