chr12-53379143-C-T

Position:

• chr12-53379143-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 0.229 in 152,084 control chromosomes in the GnomAD database, including 4,116 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 (4116 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.32 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: 0.229 AC: 34842 AN: 151966 Hom.: 4109 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.229 AC: 34871 AN: 152084 Hom.: 4116 Cov.: 32 AF XY: 0.231 AC XY: 17171 AN XY: 74316

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.228

Gnomad4 OTH AF: 0.209

Alfa AF: 0.227 Hom.: 6532

Bravo AF: 0.224

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	1.6
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7131938; hg19: chr12-53772927;