rs10519502

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.0408

Gnomad4 AMR AF: 0.0542

Gnomad4 ASJ AF: 0.0436

Gnomad4 EAS AF: 0.00887

Gnomad4 SAS AF: 0.0193

Gnomad4 FIN AF: 0.0426

Gnomad4 NFE AF: 0.0314

Gnomad4 OTH AF: 0.0312

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519502; hg19: chr5-116642215;