12-43640356-C-T

Variant names:

• chr12-43640356-C-T
• rs277203

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 0.26 in 151,216 control chromosomes in the GnomAD database, including 6,227 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 0.26 (6227 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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 (AMR) allele frequency at 95% confidence interval = 0.355 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: 0.260 AC: 39318 AN: 151102 Hom.: 6217 Cov.: 30

Gnomad AFR AF: 0.0968

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.260 AC: 39344 AN: 151216 Hom.: 6227 Cov.: 30 AF XY: 0.261 AC XY: 19254 AN XY: 73816

Gnomad4 AFR AF: 0.0967

Gnomad4 AMR AF: 0.363

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.252

Alfa AF: 0.319 Hom.: 4097

Bravo AF: 0.256

Asia WGS AF: 0.143 AC: 498 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277203; hg19: chr12-44034159;