chr12-19013890-T-G

Variant names:

• chr12-19013890-T-G
• rs9804790

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.221 in 152,078 control chromosomes in the GnomAD database, including 5,021 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 0.22 (5021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 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: 0.220 AC: 33498 AN: 151962 Hom.: 4999 Cov.: 32

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.221 AC: 33565 AN: 152078 Hom.: 5021 Cov.: 32 AF XY: 0.221 AC XY: 16454 AN XY: 74328

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.223

Alfa AF: 0.135 Hom.: 979

Bravo AF: 0.234

Asia WGS AF: 0.361 AC: 1251 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9804790; hg19: chr12-19166824;