15-53216395-A-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837531.2	n.481-5031A>G		intron_variant	Intron 4 of 4
LOC107983981	XR_932257.3	n.697-5031A>G		intron_variant	Intron 5 of 5

Ensembl

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

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 v4.3

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;