15-47917521-C-T

Position:

• chr15-47917521-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+33017C>T		intron_variant
LOC124900354	XR_001751517.2	n.142+33017C>T		intron_variant
LOC124900354	XR_001751518.3	n.82+2159C>T		intron_variant
LOC124900354	XR_007064618.1	n.143-31835C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+33017C>T		intron_variant		4
ENSG00000259754	ENST00000662551.1	n.189-75188C>T		intron_variant
ENSG00000259754	ENST00000664705.1	n.189-75188C>T		intron_variant
ENSG00000259754	ENST00000665188.1	n.69-75188C>T		intron_variant

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

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.0660

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0255

Alfa AF: 0.0190 Hom.: 42

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16960341; hg19: chr15-48209718;