rs10520033

Variant names:

• chr15-35866461-G-T
• rs10520033
• ENST00000820119.1:n.480-14147C>A

Variant summary

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

The ENST00000820119.1(ENSG00000259639):​n.480-14147C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0662 in 152,048 control chromosomes in the GnomAD database, including 765 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 0.066 (765 hom., cov: 32)
• Consequence: ENSG00000259639 ENST00000820119.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 1 publications found

Genes affected

ENSG00000259639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 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
ENSG00000259639	ENST00000820119.1	n.480-14147C>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0661 AC: 10040 AN: 151930 Hom.: 761 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0469

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0662 AC: 10065 AN: 152048 Hom.: 765 Cov.: 32 AF XY: 0.0631 AC XY: 4690 AN XY: 74326

African (AFR) AF: 0.183 AC: 7568 AN: 41446

American (AMR) AF: 0.0467 AC: 712 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 106 AN: 3464

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5174

South Asian (SAS) AF: 0.00394 AC: 19 AN: 4822

European-Finnish (FIN) AF: 0.0227 AC: 240 AN: 10594

Middle Eastern (MID) AF: 0.0514 AC: 15 AN: 292

European-Non Finnish (NFE) AF: 0.0186 AC: 1262 AN: 67972

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0544 Hom.: 126

Bravo AF: 0.0756

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	10
DANN	Benign	0.63
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs10520033; hg19: chr15-36158662;