rs10514040

Variant names:

• chr18-72147878-A-G
• rs10514040
• XR_001753545.1:n.306T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001753545.1(LOC105372189):​n.306T>C variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0872 in 152,204 control chromosomes in the GnomAD database, including 782 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 0.087 (782 hom., cov: 32)
• Consequence: LOC105372189 XR_001753545.1 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 2 publications found

Genes affected

LOC105372189 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372189	XR_001753545.1	n.306T>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0872 AC: 13266 AN: 152086 Hom.: 780 Cov.: 32

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0758

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0738

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0872 AC: 13267 AN: 152204 Hom.: 782 Cov.: 32 AF XY: 0.0881 AC XY: 6559 AN XY: 74414

African (AFR) AF: 0.0227 AC: 945 AN: 41542

American (AMR) AF: 0.118 AC: 1802 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0758 AC: 262 AN: 3458

East Asian (EAS) AF: 0.268 AC: 1387 AN: 5170

South Asian (SAS) AF: 0.124 AC: 596 AN: 4822

European-Finnish (FIN) AF: 0.0738 AC: 783 AN: 10608

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7180 AN: 68000

Other (OTH) AF: 0.0828 AC: 175 AN: 2114

Alfa AF: 0.0949 Hom.: 1008

Bravo AF: 0.0879

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	11
DANN	Benign	0.78
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10514040; hg19: chr18-69815113; COSMIC: COSV107179423;