rs10518855

Variant names:

• chr15-56536787-C-T
• rs10518855
• XR_007064652.1:n.222-39714G>A

Variant summary

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

The XR_007064652.1(LOC105370832):​n.222-39714G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0379 in 152,182 control chromosomes in the GnomAD database, including 438 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 0.038 (438 hom., cov: 31)
• Consequence: LOC105370832 XR_007064652.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 1 publications found

Genes affected

LOC105370832 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370832	XR_007064652.1	n.222-39714G>A		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0378 AC: 5747 AN: 152064 Hom.: 431 Cov.: 31

Gnomad AFR AF: 0.00969

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.0245

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0481

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

GnomAD4 genome AF: 0.0379 AC: 5768 AN: 152182 Hom.: 438 Cov.: 31 AF XY: 0.0395 AC XY: 2937 AN XY: 74394

African (AFR) AF: 0.00966 AC: 401 AN: 41510

American (AMR) AF: 0.185 AC: 2829 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0245 AC: 85 AN: 3472

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5180

South Asian (SAS) AF: 0.0326 AC: 157 AN: 4822

European-Finnish (FIN) AF: 0.0230 AC: 244 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0272 AC: 1850 AN: 67992

Other (OTH) AF: 0.0490 AC: 103 AN: 2102

Alfa AF: 0.0379 Hom.: 45

Bravo AF: 0.0520

Asia WGS AF: 0.0450 AC: 156 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.63
DANN	Benign	0.38
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10518855; hg19: chr15-56828985;