15-23779258-T-C

Variant names:

• chr15-23779258-T-C
• rs1524847
• ENST00000658937.1:n.459+21685T>C

Variant summary

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

The ENST00000658937.1(ENSG00000286973):​n.459+21685T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,152 control chromosomes in the GnomAD database, including 49,251 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 0.80 (49251 hom., cov: 33)
• Consequence: ENSG00000286973 ENST00000658937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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+21685T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122151 AN: 152034 Hom.: 49192 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.774

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.809

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.804 AC: 122269 AN: 152152 Hom.: 49251 Cov.: 33 AF XY: 0.803 AC XY: 59684 AN XY: 74352

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.774

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.810

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.833

Alfa AF: 0.798 Hom.: 6038

Bravo AF: 0.813

Asia WGS AF: 0.877 AC: 3044 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524847; hg19: chr15-24024405;