rs10519131

Positions:

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

Variant summary

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

The ENST00000559590.2(ENSG00000259675):​n.61+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 ENST00000559590.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

Genes affected

ENSG00000259675 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984782	XR_001751569.2	n.72+6182T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259675	ENST00000559590.2	n.61+6182T>G		intron_variant		3
ENSG00000259675	ENST00000662958.3	n.89+6182T>G		intron_variant
ENSG00000259675	ENST00000691967.2	n.80+6182T>G		intron_variant
ENSG00000259675	ENST00000700958.1	n.44+6182T>G		intron_variant

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

Gnomad4 AFR AF: 0.0710

Gnomad4 AMR AF: 0.0608

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0994

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.0878

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.0893

Alfa AF: 0.111 Hom.: 1161

Bravo AF: 0.0940

Asia WGS AF: 0.117 AC: 409 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519131; hg19: chr15-62001132;