rs482541

Variant names:

• chr15-53216997-A-G
• rs482541
• XR_004837531.2:n.481-4429A>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.481-4429A>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 152,154 control chromosomes in the GnomAD database, including 50,360 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 (50360 hom., cov: 33)
• Consequence: LOC107983981 XR_004837531.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 4 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.889 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: 0.805 AC: 122391 AN: 152036 Hom.: 50333 Cov.: 33

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.943

Gnomad MID AF: 0.813

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: 122461 AN: 152154 Hom.: 50360 Cov.: 33 AF XY: 0.805 AC XY: 59879 AN XY: 74392

African (AFR) AF: 0.642 AC: 26620 AN: 41452

American (AMR) AF: 0.822 AC: 12562 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.811 AC: 2816 AN: 3472

East Asian (EAS) AF: 0.584 AC: 3020 AN: 5168

South Asian (SAS) AF: 0.780 AC: 3753 AN: 4814

European-Finnish (FIN) AF: 0.943 AC: 10010 AN: 10618

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.895 AC: 60888 AN: 68026

Other (OTH) AF: 0.810 AC: 1712 AN: 2114

Alfa AF: 0.866 Hom.: 24383

Bravo AF: 0.786

Asia WGS AF: 0.687 AC: 2388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.51
DANN	Benign	0.79
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs482541; hg19: chr15-53509194;