rs10519017

chr15-60197631-G-A

Variant summary

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

The XR_932310.3(LOC105370839):n.353+17136G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,900 control chromosomes in the GnomAD database, including 1,741 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 0.13 (1741 hom., cov: 32)
• Consequence: LOC105370839 XR_932310.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

Genes affected

LOC105370839 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370839	XR_932310.3	n.353+17136G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19909 AN: 151782 Hom.: 1739 Cov.: 32

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0991

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.131 AC: 19933 AN: 151900 Hom.: 1741 Cov.: 32 AF XY: 0.126 AC XY: 9360 AN XY: 74266

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.0571

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.0791

Gnomad4 NFE AF: 0.0991

Gnomad4 OTH AF: 0.114

Alfa AF: 0.118 Hom.: 422

Bravo AF: 0.137

Asia WGS AF: 0.0320 AC: 112 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.30
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519017; hg19: chr15-60489830;