12-56937303-T-C

Position:

• chr12-56937303-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 0.129 in 152,040 control chromosomes in the GnomAD database, including 1,325 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 0.13 (1325 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.209 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: 0.129 AC: 19582 AN: 151922 Hom.: 1330 Cov.: 31

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.114

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

GnomAD4 genome AF: 0.129 AC: 19588 AN: 152040 Hom.: 1325 Cov.: 31 AF XY: 0.130 AC XY: 9648 AN XY: 74324

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.114

Alfa AF: 0.107 Hom.: 1245

Bravo AF: 0.132

Asia WGS AF: 0.162 AC: 562 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10506347; hg19: chr12-57331087;