12-43640356-C-T

Variant names:

• chr12-43640356-C-T
• rs277203

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0967 AC: 3987 AN: 41214

American (AMR) AF: 0.363 AC: 5509 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3466

East Asian (EAS) AF: 0.0387 AC: 199 AN: 5136

South Asian (SAS) AF: 0.238 AC: 1139 AN: 4788

European-Finnish (FIN) AF: 0.366 AC: 3781 AN: 10320

Middle Eastern (MID) AF: 0.191 AC: 55 AN: 288

European-Non Finnish (NFE) AF: 0.338 AC: 22946 AN: 67830

Other (OTH) AF: 0.252 AC: 528 AN: 2094

Alfa AF: 0.318 Hom.: 4522

Bravo AF: 0.256

Asia WGS AF: 0.143 AC: 498 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.69
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs277203; hg19: chr12-44034159;