rs12069782

Variant names:

• chr1-67134418-C-A
• rs12069782
• NM_001276351.2:c.-104+512G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-67134418-C-A
• chr1-67134418-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001276351.2(C1orf141):​c.-104+512G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: C1orf141 NM_001276351.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 13 publications found

Genes affected

C1orf141 (HGNC:32044): (chromosome 1 open reading frame 141)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001276351.2. 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
	C1orf141	NM_001276351.2	MANE Select	c.-104+512G>T		intron	N/A	NP_001263280.1	Q5JVX7-1
	C1orf141	NM_001276352.2		c.-104+512G>T		intron	N/A	NP_001263281.1	F2Z2X7
	C1orf141	NR_075077.2		n.41+512G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf141	ENST00000684719.1	MANE Select	c.-104+512G>T		intron	N/A	ENSP00000507487.1	Q5JVX7-1
	C1orf141	ENST00000544837.5	TSL:1	n.-104+512G>T		intron	N/A	ENSP00000444018.2	A0A0A0MTM1
	C1orf141	ENST00000371007.6	TSL:5	c.-103-3191G>T		intron	N/A	ENSP00000360046.1	Q5JVX7-1

Frequencies

GnomAD3 genomes Cov.: 34

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

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		-0.15

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs12069782; hg19: chr1-67600101;