rs10520131

Variant names:

• chr15-39486279-G-A
• rs10520131
• ENST00000654986.1:n.911+5211G>A

Variant summary

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

The ENST00000654986.1(ENSG00000259269):​n.911+5211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.083 in 152,222 control chromosomes in the GnomAD database, including 979 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 0.083 (979 hom., cov: 32)
• Consequence: ENSG00000259269 ENST00000654986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.36
• Publications: 0 publications found

Genes affected

ENSG00000259269 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259269	ENST00000654986.1	n.911+5211G>A		intron_variant	Intron 4 of 4
ENSG00000259269	ENST00000655192.1	n.901+5183G>A		intron_variant	Intron 4 of 4
ENSG00000259269	ENST00000656318.1	n.1174+5183G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.0829 AC: 12606 AN: 152104 Hom.: 975 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0388

Gnomad ASJ AF: 0.0300

Gnomad EAS AF: 0.0354

Gnomad SAS AF: 0.0524

Gnomad FIN AF: 0.0150

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0332

Gnomad OTH AF: 0.0699

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

GnomAD4 genome AF: 0.0830 AC: 12628 AN: 152222 Hom.: 979 Cov.: 32 AF XY: 0.0795 AC XY: 5920 AN XY: 74444

African (AFR) AF: 0.213 AC: 8854 AN: 41502

American (AMR) AF: 0.0387 AC: 592 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0300 AC: 104 AN: 3472

East Asian (EAS) AF: 0.0353 AC: 183 AN: 5184

South Asian (SAS) AF: 0.0528 AC: 255 AN: 4826

European-Finnish (FIN) AF: 0.0150 AC: 159 AN: 10614

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0332 AC: 2261 AN: 68018

Other (OTH) AF: 0.0687 AC: 145 AN: 2110

Alfa AF: 0.0522 Hom.: 179

Bravo AF: 0.0919

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.5
DANN	Benign	0.71
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs10520131; hg19: chr15-39778480;