rs10492225

Positions:

• chr12-96067528-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;