12-121122778-C-T

Position:

• chr12-121122778-C-T

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 0.596 in 151,794 control chromosomes in the GnomAD database, including 30,755 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 0.60 (30755 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.754 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: 0.597 AC: 90515 AN: 151674 Hom.: 30766 Cov.: 29

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.801

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.596 AC: 90506 AN: 151794 Hom.: 30755 Cov.: 29 AF XY: 0.599 AC XY: 44392 AN XY: 74170

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.617

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.664

Alfa AF: 0.731 Hom.: 55130

Bravo AF: 0.594

Asia WGS AF: 0.588 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208277; hg19: chr12-121560581;