rs10492225

Variant names:

• chr12-96067528-T-C
• rs10492225

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0292 AC: 1214 AN: 41516

American (AMR) AF: 0.228 AC: 3482 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3464

East Asian (EAS) AF: 0.147 AC: 764 AN: 5184

South Asian (SAS) AF: 0.0502 AC: 242 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1697 AN: 10542

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 9979 AN: 67980

Other (OTH) AF: 0.137 AC: 289 AN: 2110

Alfa AF: 0.137 Hom.: 1129

Bravo AF: 0.128

Asia WGS AF: 0.0850 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.1
DANN	Benign	0.79
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs10492225; hg19: chr12-96461306;