chr12-33150676-G-C

Position:

• chr12-33150676-G-C

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 0.203 in 143,664 control chromosomes in the GnomAD database, including 7,224 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 0.20 (7224 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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: 0.203 AC: 29122 AN: 143538 Hom.: 7206 Cov.: 28

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.0875

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.0806

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.203 AC: 29185 AN: 143664 Hom.: 7224 Cov.: 28 AF XY: 0.212 AC XY: 14846 AN XY: 70020

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.874

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.0806

Gnomad4 NFE AF: 0.0895

Gnomad4 OTH AF: 0.199

Alfa AF: 0.148 Hom.: 564

Asia WGS AF: 0.592 AC: 1979 AN: 3354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.4
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7972327; hg19: chr12-33303610;