rs10515593

Variant names:

• chr5-147819237-C-T
• rs10515593

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 0.164 in 152,066 control chromosomes in the GnomAD database, including 2,519 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 0.16 (2519 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.219 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

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24903 AN: 151948 Hom.: 2520 Cov.: 33

Gnomad AFR AF: 0.0678

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.164 AC: 24898 AN: 152066 Hom.: 2519 Cov.: 33 AF XY: 0.165 AC XY: 12243 AN XY: 74318

Gnomad4 AFR AF: 0.0676

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0467

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.159

Alfa AF: 0.202 Hom.: 459

Bravo AF: 0.145

Asia WGS AF: 0.114 AC: 395 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.90
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515593; hg19: chr5-147198800;