rs10512876

chr5-45249502-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 0.0493 in 152,274 control chromosomes in the GnomAD database, including 447 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 0.049 (447 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.385

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.325 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: 0.0493 AC: 7495 AN: 152156 Hom.: 444 Cov.: 32

Gnomad AFR AF: 0.00878

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0357

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.0949

Gnomad FIN AF: 0.0919

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0456

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0493 AC: 7502 AN: 152274 Hom.: 447 Cov.: 32 AF XY: 0.0545 AC XY: 4057 AN XY: 74456

Gnomad4 AFR AF: 0.00876

Gnomad4 AMR AF: 0.0361

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.0946

Gnomad4 FIN AF: 0.0919

Gnomad4 NFE AF: 0.0456

Gnomad4 OTH AF: 0.0406

Alfa AF: 0.0447 Hom.: 283

Bravo AF: 0.0442

Asia WGS AF: 0.176 AC: 612 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	4.4
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512876; hg19: chr5-45249604;