rs10512924

chr5-51182216-G-Achr5-51182216-G-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 0.91 in 152,260 control chromosomes in the GnomAD database, including 63,220 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 0.91 (63220 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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 (EAS) allele frequency at 95% confidence interval = 0.972 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: 0.910 AC: 138511 AN: 152142 Hom.: 63158 Cov.: 33

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.910 AC: 138631 AN: 152260 Hom.: 63220 Cov.: 33 AF XY: 0.915 AC XY: 68078 AN XY: 74434

Gnomad4 AFR AF: 0.927

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.935

Gnomad4 NFE AF: 0.887

Gnomad4 OTH AF: 0.903

Alfa AF: 0.902 Hom.: 12579

Bravo AF: 0.909

Asia WGS AF: 0.951 AC: 3297 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.24
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512924; hg19: chr5-50478050;