12-56935476-C-T

Variant names:

• chr12-56935476-C-T
• rs7358723

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 0.0388 in 152,186 control chromosomes in the GnomAD database, including 566 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 0.039 (566 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0388 AC: 5907 AN: 152068 Hom.: 563 Cov.: 32

Gnomad AFR AF: 0.00626

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.0610

Gnomad FIN AF: 0.0476

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0388 AC: 5912 AN: 152186 Hom.: 566 Cov.: 32 AF XY: 0.0439 AC XY: 3263 AN XY: 74378

Gnomad4 AFR AF: 0.00624

Gnomad4 AMR AF: 0.0890

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.0619

Gnomad4 FIN AF: 0.0476

Gnomad4 NFE AF: 0.0165

Gnomad4 OTH AF: 0.0506

Alfa AF: 0.0220 Hom.: 17

Bravo AF: 0.0448

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	13
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7358723; hg19: chr12-57329260;