chr12-23278623-T-G

Position:

• chr12-23278623-T-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 0.872 in 152,136 control chromosomes in the GnomAD database, including 59,755 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 0.87 (59755 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132542 AN: 152018 Hom.: 59725 Cov.: 31

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.934

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.947

Gnomad FIN AF: 0.983

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.872 AC: 132620 AN: 152136 Hom.: 59755 Cov.: 31 AF XY: 0.875 AC XY: 65045 AN XY: 74366

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.930

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.948

Gnomad4 FIN AF: 0.983

Gnomad4 NFE AF: 0.977

Gnomad4 OTH AF: 0.891

Alfa AF: 0.941 Hom.: 29422

Bravo AF: 0.857

Asia WGS AF: 0.940 AC: 3269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.3
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4321001; hg19: chr12-23431557;