rs1169313

Variant names:

• chr12-121004867-T-A
• rs1169313
• NM_022895.3:c.452+136A>T

Your query was ambiguous. Multiple possible variants found:

• chr12-121004867-T-A
• chr12-121004867-T-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_022895.3(C12orf43):​c.452+136A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000128 in 601,200 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000053 (0 hom., cov: 31)
  • Exomes 𝑓: 0.00015 (0 hom.)
• Consequence: C12orf43 NM_022895.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291
• Publications: 46 publications found

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]

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022895.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf43	NM_022895.3	MANE Select	c.452+136A>T		intron	N/A	NP_075046.1
	C12orf43	NM_001286191.2		c.545+136A>T		intron	N/A	NP_001273120.1	F5H7W8
	C12orf43	NM_001286192.2		c.452+136A>T		intron	N/A	NP_001273121.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C12orf43	ENST00000288757.7	TSL:1 MANE Select	c.452+136A>T		intron	N/A	ENSP00000288757.5	Q96C57
	C12orf43	ENST00000537817.5	TSL:1	c.545+136A>T		intron	N/A	ENSP00000442224.2	F5H7W8
	C12orf43	ENST00000886556.1		c.545+136A>T		intron	N/A	ENSP00000556615.1

Frequencies

GnomAD3 genomes AF: 0.0000527 AC: 8 AN: 151928 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000154 AC: 69 AN: 449154 Hom.: 0 AF XY: 0.000106 AC XY: 24 AN XY: 226684

African (AFR) AF: 0.00 AC: 0 AN: 10638

American (AMR) AF: 0.00 AC: 0 AN: 11240

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11310

East Asian (EAS) AF: 0.00267 AC: 69 AN: 25818

South Asian (SAS) AF: 0.00 AC: 0 AN: 19650

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37748

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1786

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 307222

Other (OTH) AF: 0.00 AC: 0 AN: 23742

GnomAD4 genome AF: 0.0000526 AC: 8 AN: 152046 Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4 AN XY: 74298

African (AFR) AF: 0.00 AC: 0 AN: 41486

American (AMR) AF: 0.00 AC: 0 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5162

South Asian (SAS) AF: 0.00 AC: 0 AN: 4810

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10568

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67960

Other (OTH) AF: 0.00 AC: 0 AN: 2110

Alfa AF: 0.00 Hom.: 12884

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.8
DANN	Benign	0.56
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1169313; hg19: chr12-121442670;