rs10514013

chr18-71487494-A-G

Variant summary

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

The XR_001753502.1(LOC107985179):n.64+55346A>G 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 0.0538 in 151,784 control chromosomes in the GnomAD database, including 319 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 0.054 (319 hom., cov: 31)
• Consequence: LOC107985179 XR_001753502.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

Genes affected

LOC107985179 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985179	XR_001753502.1	n.64+55346A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0538 AC: 8165 AN: 151664 Hom.: 320 Cov.: 31

Gnomad AFR AF: 0.0106

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.0608

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.0467

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

GnomAD4 genome AF: 0.0538 AC: 8170 AN: 151784 Hom.: 319 Cov.: 31 AF XY: 0.0567 AC XY: 4206 AN XY: 74180

Gnomad4 AFR AF: 0.0106

Gnomad4 AMR AF: 0.0261

Gnomad4 ASJ AF: 0.0608

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.0481

Alfa AF: 0.0623 Hom.: 486

Bravo AF: 0.0429

Asia WGS AF: 0.122 AC: 425 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.3
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10514013; hg19: chr18-69154730;