rs10515593

Positions:

• chr5-147819237-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;