rs10492189

chr12-16627167-A-G

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 0.0302 in 152,222 control chromosomes in the GnomAD database, including 175 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 0.030 (175 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0820

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0301 AC: 4584 AN: 152104 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0922

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00514

Gnomad OTH AF: 0.0220

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

GnomAD4 genome AF: 0.0302 AC: 4600 AN: 152222 Hom.: 175 Cov.: 32 AF XY: 0.0297 AC XY: 2209 AN XY: 74418

Gnomad4 AFR AF: 0.0923

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00514

Gnomad4 OTH AF: 0.0218

Alfa AF: 0.0166 Hom.: 21

Bravo AF: 0.0331

Asia WGS AF: 0.0110 AC: 38 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492189; hg19: chr12-16780101;