rs10512924

Variant names:

• chr5-51182216-G-A
• rs10512924

Your query was ambiguous. Multiple possible variants found:

• chr5-51182216-G-A
• chr5-51182216-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.927 AC: 38499 AN: 41548

American (AMR) AF: 0.913 AC: 13965 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.909 AC: 3154 AN: 3470

East Asian (EAS) AF: 0.995 AC: 5157 AN: 5182

South Asian (SAS) AF: 0.957 AC: 4621 AN: 4830

European-Finnish (FIN) AF: 0.935 AC: 9911 AN: 10596

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60359 AN: 68024

Other (OTH) AF: 0.903 AC: 1908 AN: 2114

Alfa AF: 0.903 Hom.: 12906

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10512924; hg19: chr5-50478050;