12-56805570-C-T

Position:

• chr12-56805570-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 0.157 in 152,206 control chromosomes in the GnomAD database, including 2,595 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 0.16 (2595 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 (NFE) allele frequency at 95% confidence interval = 0.234 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: 0.157 AC: 23866 AN: 152088 Hom.: 2594 Cov.: 32

Gnomad AFR AF: 0.0445

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.157 AC: 23857 AN: 152206 Hom.: 2595 Cov.: 32 AF XY: 0.150 AC XY: 11158 AN XY: 74432

Gnomad4 AFR AF: 0.0444

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.281

Gnomad4 EAS AF: 0.00232

Gnomad4 SAS AF: 0.0839

Gnomad4 FIN AF: 0.136

Gnomad4 NFE AF: 0.238

Gnomad4 OTH AF: 0.192

Alfa AF: 0.0531 Hom.: 52

Bravo AF: 0.157

Asia WGS AF: 0.0360 AC: 128 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	6.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870673; hg19: chr12-57199354;