12-121607669-T-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 0.234 in 151,934 control chromosomes in the GnomAD database, including 4,457 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 0.23 (4457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.234 AC: 35578 AN: 151816 Hom.: 4451 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.0974

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.234 AC: 35605 AN: 151934 Hom.: 4457 Cov.: 32 AF XY: 0.231 AC XY: 17178 AN XY: 74274

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.155

Gnomad4 EAS AF: 0.0976

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.197

Alfa AF: 0.206 Hom.: 3386

Bravo AF: 0.229

Asia WGS AF: 0.100 AC: 353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
Cadd	Benign	7.8
Dann	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7962930; hg19: chr12-122045574;