Variant rs2258287 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The 12-121016510-C-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 1,611,520 control chromosomes in the GnomAD database, including 102,540 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 0.35 ( 9698 hom., cov: 34)

Exomes 𝑓: 0.35 ( 92842 hom. )

Consequence

C12orf43
NM_022895.3 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.216

Variant links:

Genes affected

C12orf43 (HGNC:25719): (chromosome 12 open reading frame 43) Predicted to be involved in Spemann organizer formation and negative regulation of Wnt signaling pathway. Predicted to be located in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

C12orf43 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C12orf43	NM_022895.3 linkuse as main transcript			upstream_gene_variant		ENST00000288757.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C12orf43	ENST00000288757.7 linkuse as main transcript			upstream_gene_variant		1	NM_022895.3	P2

Frequencies

GnomAD3 genomes

AF:

0.346

AC:

52540

AN:

152036

Hom.:

9688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.294

Gnomad AMI

AF:

0.499

Gnomad AMR

AF:

0.376

Gnomad ASJ

AF:

0.471

Gnomad EAS

AF:

0.735

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.333

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.322

Gnomad OTH

AF:

0.361

GnomAD3 exomes

AF:

0.395

AC:

98558

AN:

249496

Hom.:

21334

AF XY:

0.399

AC XY:

53848

AN XY:

134956

show subpopulations

Gnomad AFR exome

AF:

0.292

Gnomad AMR exome

AF:

0.390

Gnomad ASJ exome

AF:

0.473

Gnomad EAS exome

AF:

0.738

Gnomad SAS exome

AF:

0.499

Gnomad FIN exome

AF:

0.329

Gnomad NFE exome

AF:

0.333

Gnomad OTH exome

AF:

0.380

GnomAD4 exome

AF:

0.347

AC:

506015

AN:

1459366

Hom.:

92842

Cov.:

AF XY:

0.352

AC XY:

255134

AN XY:

725774

show subpopulations

Gnomad4 AFR exome

AF:

0.287

Gnomad4 AMR exome

AF:

0.391

Gnomad4 ASJ exome

AF:

0.478

Gnomad4 EAS exome

AF:

0.720

Gnomad4 SAS exome

AF:

0.491

Gnomad4 FIN exome

AF:

0.325

Gnomad4 NFE exome

AF:

0.318

Gnomad4 OTH exome

AF:

0.377

GnomAD4 genome

AF:

0.346

AC:

52581

AN:

152154

Hom.:

9698

Cov.:

AF XY:

0.354

AC XY:

26343

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.294

Gnomad4 AMR

AF:

0.376

Gnomad4 ASJ

AF:

0.471

Gnomad4 EAS

AF:

0.734

Gnomad4 SAS

AF:

0.499

Gnomad4 FIN

AF:

0.333

Gnomad4 NFE

AF:

0.322

Gnomad4 OTH

AF:

0.366

Alfa

AF:

0.307

Hom.:

2517

Bravo

AF:

0.347

Asia WGS

AF:

0.615

AC:

2133

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.7

DANN

Benign

0.67

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over