15-47937403-T-C

Position:

• chr15-47937403-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560900.1(ENSG00000259754):​n.195+52899T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,152 control chromosomes in the GnomAD database, including 9,002 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 0.32 (9002 hom., cov: 33)
• Consequence: ENSG00000259754 ENST00000560900.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493

Genes affected

ENSG00000259754 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+52899T>C		intron_variant
LOC124900354	XR_001751517.2	n.142+52899T>C		intron_variant
LOC124900354	XR_001751518.3	n.82+22041T>C		intron_variant
LOC124900354	XR_007064618.1	n.143-11953T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+52899T>C		intron_variant		4
ENSG00000259754	ENST00000662551.1	n.189-55306T>C		intron_variant
ENSG00000259754	ENST00000664705.1	n.189-55306T>C		intron_variant
ENSG00000259754	ENST00000665188.1	n.69-55306T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48741 AN: 152034 Hom.: 9007 Cov.: 33

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.320 AC: 48740 AN: 152152 Hom.: 9002 Cov.: 33 AF XY: 0.321 AC XY: 23849 AN XY: 74394

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.359

Alfa AF: 0.399 Hom.: 18540

Bravo AF: 0.313

Asia WGS AF: 0.214 AC: 744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1453854; hg19: chr15-48229600;