15-23779258-T-C

Variant names:

• chr15-23779258-T-C
• rs1524847
• ENST00000658937.2:n.509+21685T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658937.2(ENSG00000286973):​n.509+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 ENST00000658937.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.599
• Publications: 0 publications found

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000658937.2	n.509+21685T>C		intron_variant	Intron 1 of 2
ENSG00000286973	ENST00000844005.1	n.600+7478T>C		intron_variant	Intron 2 of 3
ENSG00000286973	ENST00000844006.1	n.471+21685T>C		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.774 AC: 32107 AN: 41508

American (AMR) AF: 0.857 AC: 13105 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.774 AC: 2684 AN: 3466

East Asian (EAS) AF: 0.959 AC: 4968 AN: 5178

South Asian (SAS) AF: 0.810 AC: 3906 AN: 4822

European-Finnish (FIN) AF: 0.767 AC: 8099 AN: 10564

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54597 AN: 68008

Other (OTH) AF: 0.833 AC: 1757 AN: 2108

Alfa AF: 0.797 Hom.: 6266

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
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1524847; hg19: chr15-24024405;