rs10512932

chr5-7934537-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;