chr15-23780723-A-C

Variant names:

• chr15-23780723-A-C
• rs1524846
• ENST00000658937.2:n.509+23150A>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+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 ENST00000658937.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658937.2. 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
	ENSG00000286973	ENST00000658937.2		n.509+23150A>C		intron	N/A
	ENSG00000286973	ENST00000844005.1		n.600+8943A>C		intron	N/A
	ENSG00000286973	ENST00000844006.1		n.471+23150A>C		intron	N/A

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

African (AFR) AF: 0.154 AC: 6404 AN: 41558

American (AMR) AF: 0.0245 AC: 375 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0104 AC: 36 AN: 3472

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0681 AC: 329 AN: 4828

European-Finnish (FIN) AF: 0.0104 AC: 111 AN: 10628

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0158 AC: 1072 AN: 68042

Other (OTH) AF: 0.0393 AC: 83 AN: 2110

Alfa AF: 0.0376 Hom.: 412

Bravo AF: 0.0598

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.86
DANN	Benign	0.65
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs1524846; hg19: chr15-24025870;