rs10512932

Variant names:

• chr5-7934537-A-G
• rs10512932

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 0.193 in 152,240 control chromosomes in the GnomAD database, including 3,008 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 0.19 (3008 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.358 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: 0.193 AC: 29349 AN: 152122 Hom.: 3007 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.193 AC: 29357 AN: 152240 Hom.: 3008 Cov.: 32 AF XY: 0.194 AC XY: 14418 AN XY: 74428

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.304

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.244

Alfa AF: 0.194 Hom.: 384

Bravo AF: 0.189

Asia WGS AF: 0.286 AC: 993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512932; hg19: chr5-7934650;