rs10492267

Variant names:

• chr12-97955560-G-A
• rs10492267

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 0.112 in 151,970 control chromosomes in the GnomAD database, including 1,511 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 0.11 (1511 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.112 AC: 16937 AN: 151854 Hom.: 1501 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.0641

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0507

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.112 AC: 16966 AN: 151970 Hom.: 1511 Cov.: 32 AF XY: 0.120 AC XY: 8939 AN XY: 74252

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.0641

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.273

Gnomad4 FIN AF: 0.0836

Gnomad4 NFE AF: 0.0507

Gnomad4 OTH AF: 0.131

Alfa AF: 0.0857 Hom.: 237

Bravo AF: 0.121

Asia WGS AF: 0.381 AC: 1321 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492267; hg19: chr12-98349338;