15-23805058-T-C

Variant names:

• chr15-23805058-T-C
• rs10519449
• ENST00000658937.2:n.510-19666T>C

Variant summary

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

The ENST00000658937.2(ENSG00000286973):​n.510-19666T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 151,048 control chromosomes in the GnomAD database, including 2,357 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 0.16 (2357 hom., cov: 32)
• Consequence: ENSG00000286973 ENST00000658937.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338
• 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 = 0.268 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.510-19666T>C		intron	N/A
	ENSG00000286973	ENST00000844005.1		n.601-19666T>C		intron	N/A
	ENSG00000286973	ENST00000844006.1		n.472-19666T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24656 AN: 150930 Hom.: 2346 Cov.: 32

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0565

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.163 AC: 24686 AN: 151048 Hom.: 2357 Cov.: 32 AF XY: 0.158 AC XY: 11669 AN XY: 73876

African (AFR) AF: 0.272 AC: 11267 AN: 41386

American (AMR) AF: 0.142 AC: 2138 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3462

East Asian (EAS) AF: 0.0306 AC: 158 AN: 5170

South Asian (SAS) AF: 0.0553 AC: 267 AN: 4832

European-Finnish (FIN) AF: 0.110 AC: 1168 AN: 10578

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.130 AC: 8747 AN: 67220

Other (OTH) AF: 0.171 AC: 359 AN: 2100

Alfa AF: 0.111 Hom.: 355

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.93
DANN	Benign	0.42
PhyloP100		-0.34

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: rs10519449;

hg19: chr15-24050205;