15-47937403-T-C

Variant names:

• chr15-47937403-T-C
• rs1453854
• ENST00000560900.1:n.195+52899T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 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=-0.9).
• 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 rank	MANE	Protein	UniProt
LOC124900354	XR_001751516.3	n.142+52899T>C		intron_variant	Intron 1 of 2
LOC124900354	XR_001751517.2	n.142+52899T>C		intron_variant	Intron 1 of 2
LOC124900354	XR_001751518.3	n.82+22041T>C		intron_variant	Intron 1 of 2
LOC124900354	XR_007064618.1	n.143-11953T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259754	ENST00000560900.1	n.195+52899T>C		intron_variant	Intron 1 of 2	4
ENSG00000259754	ENST00000662551.1	n.189-55306T>C		intron_variant	Intron 1 of 2
ENSG00000259754	ENST00000664705.1	n.189-55306T>C		intron_variant	Intron 1 of 5

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

African (AFR) AF: 0.140 AC: 5822 AN: 41536

American (AMR) AF: 0.371 AC: 5676 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1559 AN: 3468

East Asian (EAS) AF: 0.162 AC: 840 AN: 5188

South Asian (SAS) AF: 0.303 AC: 1464 AN: 4826

European-Finnish (FIN) AF: 0.386 AC: 4081 AN: 10576

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.412 AC: 27979 AN: 67958

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.381 Hom.: 27625

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
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1453854; hg19: chr15-48229600;