rs10519502

Variant names:

• chr5-117306519-T-A
• rs10519502
• ENST00000762793.1:n.472-2474T>A

Your query was ambiguous. Multiple possible variants found:

• chr5-117306519-T-A
• chr5-117306519-T-C

Variant summary

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

The ENST00000762793.1(ENSG00000299350):​n.472-2474T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 152,328 control chromosomes in the GnomAD database, including 110 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 0.036 (110 hom., cov: 32)
• Consequence: ENSG00000299350 ENST00000762793.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 0 publications found

Genes affected

ENSG00000299350 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0512 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
ENSG00000299350	ENST00000762793.1	n.472-2474T>A		intron_variant	Intron 2 of 2
ENSG00000299350	ENST00000762794.1	n.820-2474T>A		intron_variant	Intron 2 of 2
ENSG00000299350	ENST00000762796.1	n.129-2474T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 5459 AN: 152210 Hom.: 105 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0536

Gnomad ASJ AF: 0.0436

Gnomad EAS AF: 0.00904

Gnomad SAS AF: 0.0193

Gnomad FIN AF: 0.0426

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0315

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

GnomAD4 genome AF: 0.0360 AC: 5490 AN: 152328 Hom.: 110 Cov.: 32 AF XY: 0.0365 AC XY: 2720 AN XY: 74472

African (AFR) AF: 0.0408 AC: 1697 AN: 41580

American (AMR) AF: 0.0542 AC: 830 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0436 AC: 151 AN: 3466

East Asian (EAS) AF: 0.00887 AC: 46 AN: 5186

South Asian (SAS) AF: 0.0193 AC: 93 AN: 4824

European-Finnish (FIN) AF: 0.0426 AC: 452 AN: 10614

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0314 AC: 2135 AN: 68030

Other (OTH) AF: 0.0312 AC: 66 AN: 2116

Alfa AF: 0.00943 Hom.: 1

Bravo AF: 0.0381

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.70
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs10519502; hg19: chr5-116642215;