chr15-56536787-C-T

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;