rs10492267

Positions:

• chr12-97955560-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.97955560G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;