rs10492225

Variant names:

• chr12-96067528-T-C
• rs10492225

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 0.121 in 152,064 control chromosomes in the GnomAD database, including 1,475 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 0.12 (1475 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.222 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: 0.121 AC: 18381 AN: 151946 Hom.: 1469 Cov.: 31

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.0501

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.121 AC: 18389 AN: 152064 Hom.: 1475 Cov.: 31 AF XY: 0.123 AC XY: 9113 AN XY: 74322

Gnomad4 AFR AF: 0.0292

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0502

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.147

Gnomad4 OTH AF: 0.137

Alfa AF: 0.135 Hom.: 750

Bravo AF: 0.128

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492225; hg19: chr12-96461306;