rs10503027

chr18-59403146-C-T

Variant summary

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

The XR_001753470.1(LOC107985156):n.205G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0859 in 151,840 control chromosomes in the GnomAD database, including 715 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 0.086 (715 hom., cov: 31)
• Consequence: LOC107985156 XR_001753470.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0660

Genes affected

LOC107985156 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107985156	XR_001753470.1	n.205G>A		non_coding_transcript_exon_variant	1/9

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0859 AC: 13032 AN: 151722 Hom.: 712 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.0646

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.0104

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0521

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0859 AC: 13050 AN: 151840 Hom.: 715 Cov.: 31 AF XY: 0.0849 AC XY: 6299 AN XY: 74220

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.0738

Gnomad4 EAS AF: 0.0103

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0521

Gnomad4 NFE AF: 0.0677

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0705 Hom.: 570

Bravo AF: 0.0878

Asia WGS AF: 0.0630 AC: 222 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	3.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10503027; hg19: chr18-57070378;