rs10492034

chr12-125676150-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 0.0429 in 152,324 control chromosomes in the GnomAD database, including 204 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 0.043 (204 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0547 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: 0.0430 AC: 6541 AN: 152206 Hom.: 204 Cov.: 33

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0580

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.101

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0540

Gnomad OTH AF: 0.0468

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

GnomAD4 genome AF: 0.0429 AC: 6537 AN: 152324 Hom.: 204 Cov.: 33 AF XY: 0.0445 AC XY: 3312 AN XY: 74480

Gnomad4 AFR AF: 0.0123

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0159

Gnomad4 FIN AF: 0.101

Gnomad4 NFE AF: 0.0540

Gnomad4 OTH AF: 0.0463

Alfa AF: 0.0522 Hom.: 144

Bravo AF: 0.0414

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.8
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492034; hg19: chr12-126160696;