chr12-68254842-A-G

Position:

• chr12-68254842-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 0.366 in 152,078 control chromosomes in the GnomAD database, including 10,341 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 0.37 (10341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0670

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 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: 0.366 AC: 55577 AN: 151960 Hom.: 10330 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.405

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.371

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.366 AC: 55622 AN: 152078 Hom.: 10341 Cov.: 32 AF XY: 0.367 AC XY: 27298 AN XY: 74314

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.398

Alfa AF: 0.376 Hom.: 18599

Bravo AF: 0.364

Asia WGS AF: 0.333 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2227478; hg19: chr12-68648622;