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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000560900.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259754	ENST00000560900.1	TSL:4	n.195+52899T>C		intron	N/A
	ENSG00000259754	ENST00000662551.1		n.189-55306T>C		intron	N/A
	ENSG00000259754	ENST00000664705.1		n.189-55306T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1453854;

hg19: chr15-48229600;