5-51015242-G-T

Variant names:

• chr5-51015242-G-T
• rs10512927

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 0.16 in 152,134 control chromosomes in the GnomAD database, including 2,201 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 (2201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.227 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: 0.160 AC: 24281 AN: 152016 Hom.: 2199 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.160 AC: 24286 AN: 152134 Hom.: 2201 Cov.: 32 AF XY: 0.157 AC XY: 11678 AN XY: 74388

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0588

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.202

Alfa AF: 0.104 Hom.: 199

Bravo AF: 0.167

Asia WGS AF: 0.0950 AC: 331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512927; hg19: chr5-50311076;