rs1524846

Variant names:

• chr15-23780723-A-C
• rs1524846
• ENST00000658937.1:n.459+23150A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-23780723-A-C
• chr15-23780723-A-T

Variant summary

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

The ENST00000658937.1(ENSG00000286973):​n.459+23150A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,340 control chromosomes in the GnomAD database, including 522 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 0.055 (522 hom., cov: 32)
• Consequence: ENSG00000286973 ENST00000658937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

ENSG00000286973 (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 (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286973	ENST00000658937.1	n.459+23150A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8413 AN: 152222 Hom.: 519 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0104

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0158

Gnomad OTH AF: 0.0388

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

GnomAD4 genome AF: 0.0553 AC: 8420 AN: 152340 Hom.: 522 Cov.: 32 AF XY: 0.0541 AC XY: 4034 AN XY: 74506

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0245

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0681

Gnomad4 FIN AF: 0.0104

Gnomad4 NFE AF: 0.0158

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0188 Hom.: 70

Bravo AF: 0.0598

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524846; hg19: chr15-24025870;