chr15-87152280-G-A

Variant names:

• chr15-87152280-G-A
• rs11636768
• XR_932582.2:n.167-25947G>A

Variant summary

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

The XR_932582.2(LOC105370955):​n.167-25947G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 152,154 control chromosomes in the GnomAD database, including 1,197 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 0.11 (1197 hom., cov: 32)
• Consequence: LOC105370955 XR_932582.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.970
• Publications: 10 publications found

Genes affected

LOC105370955 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 17013 AN: 152034 Hom.: 1198 Cov.: 32

Gnomad AFR AF: 0.0361

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.112 AC: 17007 AN: 152154 Hom.: 1197 Cov.: 32 AF XY: 0.111 AC XY: 8254 AN XY: 74370

African (AFR) AF: 0.0361 AC: 1498 AN: 41536

American (AMR) AF: 0.106 AC: 1624 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3468

East Asian (EAS) AF: 0.0542 AC: 280 AN: 5166

South Asian (SAS) AF: 0.171 AC: 823 AN: 4818

European-Finnish (FIN) AF: 0.126 AC: 1328 AN: 10580

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10370 AN: 67976

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.141 Hom.: 7034

Bravo AF: 0.105

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	9.0
DANN	Benign	0.67
PhyloP100		0.97

Splicing

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

Other links and lift over

dbSNP: rs11636768; hg19: chr15-87695511;