rs10492189

Variant names:

• chr12-16627167-A-G
• rs10492189

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 0.0302 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0923 AC: 3831 AN: 41498

American (AMR) AF: 0.0118 AC: 180 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5180

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4828

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10612

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00514 AC: 350 AN: 68028

Other (OTH) AF: 0.0218 AC: 46 AN: 2110

Alfa AF: 0.0157 Hom.: 25

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
PhyloP100		-0.082

Splicing

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

Other links and lift over

dbSNP: rs10492189; hg19: chr12-16780101;