rs10503027

Variant names:

• chr18-59403146-C-T
• rs10503027
• XR_001753470.1:n.205G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

LOC107985156 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107985156	XR_001753470.1	n.205G>A		non_coding_transcript_exon_variant	Exon 1 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299960	ENST00000767705.1	n.99-427G>A		intron_variant	Intron 1 of 5
ENSG00000299960	ENST00000767706.1	n.99-427G>A		intron_variant	Intron 1 of 4
ENSG00000299960	ENST00000767710.1	n.99-427G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.142 AC: 5870 AN: 41340

American (AMR) AF: 0.0649 AC: 988 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3468

East Asian (EAS) AF: 0.0103 AC: 53 AN: 5168

South Asian (SAS) AF: 0.106 AC: 505 AN: 4772

European-Finnish (FIN) AF: 0.0521 AC: 551 AN: 10572

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0677 AC: 4605 AN: 67988

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0738 Hom.: 1417

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
PhyloP100		-0.066

Splicing

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

Other links and lift over

dbSNP: rs10503027; hg19: chr18-57070378;