rs10519131

Variant names:

• chr15-61708933-A-C
• rs10519131
• ENST00000559590.3:n.102+6182T>G

Your query was ambiguous. Multiple possible variants found:

• chr15-61708933-A-C
• chr15-61708933-A-T

Variant summary

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

The ENST00000559590.3(ENSG00000259675):​n.102+6182T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0983 in 152,280 control chromosomes in the GnomAD database, including 845 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 0.098 (845 hom., cov: 33)
• Consequence: ENSG00000259675 ENST00000559590.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 12 publications found

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559590.3. 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
	ENSG00000259675	ENST00000559590.3	TSL:3	n.102+6182T>G		intron	N/A
	ENSG00000259675	ENST00000662958.4		n.89+6182T>G		intron	N/A
	ENSG00000259675	ENST00000691967.3		n.91+6182T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14967 AN: 152162 Hom.: 846 Cov.: 33

Gnomad AFR AF: 0.0710

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0992

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0878

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.0893

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

GnomAD4 genome AF: 0.0983 AC: 14973 AN: 152280 Hom.: 845 Cov.: 33 AF XY: 0.0973 AC XY: 7248 AN XY: 74454

African (AFR) AF: 0.0710 AC: 2950 AN: 41548

American (AMR) AF: 0.0608 AC: 930 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.130 AC: 452 AN: 3472

East Asian (EAS) AF: 0.0994 AC: 515 AN: 5182

South Asian (SAS) AF: 0.166 AC: 799 AN: 4822

European-Finnish (FIN) AF: 0.0878 AC: 931 AN: 10608

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8067 AN: 68024

Other (OTH) AF: 0.0893 AC: 189 AN: 2116

Alfa AF: 0.111 Hom.: 2488

Bravo AF: 0.0940

Asia WGS AF: 0.117 AC: 409 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.40
PhyloP100		0.20

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: rs10519131;

hg19: chr15-62001132;