XR_004837531.2:n.481-5031A>G

Variant names:

• chr15-53216395-A-G
• rs566369
• XR_004837531.2:n.481-5031A>G

Variant summary

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

The XR_004837531.2(LOC107983981):​n.481-5031A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.805 in 152,034 control chromosomes in the GnomAD database, including 50,322 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 0.80 (50322 hom., cov: 30)
• Consequence: LOC107983981 XR_004837531.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.789
• Publications: 6 publications found

Genes affected

LOC107983981 (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 (NFE) allele frequency at 95% confidence interval = 0.889 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: 0.805 AC: 122297 AN: 151916 Hom.: 50296 Cov.: 30

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.895

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.805 AC: 122366 AN: 152034 Hom.: 50322 Cov.: 30 AF XY: 0.805 AC XY: 59836 AN XY: 74338

African (AFR) AF: 0.642 AC: 26584 AN: 41414

American (AMR) AF: 0.822 AC: 12565 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2816 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3018 AN: 5156

South Asian (SAS) AF: 0.779 AC: 3743 AN: 4802

European-Finnish (FIN) AF: 0.943 AC: 9986 AN: 10592

Middle Eastern (MID) AF: 0.818 AC: 239 AN: 292

European-Non Finnish (NFE) AF: 0.895 AC: 60863 AN: 67994

Other (OTH) AF: 0.809 AC: 1711 AN: 2114

Alfa AF: 0.866 Hom.: 25601

Bravo AF: 0.786

Asia WGS AF: 0.687 AC: 2391 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	0.49
DANN	Benign	0.40
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs566369; hg19: chr15-53508592;