1-67134418-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001276351.2(C1orf141):​c.-104+512G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 152,282 control chromosomes in the GnomAD database, including 51,973 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 0.83 (51973 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 is higher than 0.05.

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>A		intron	N/A	NP_001263280.1	Q5JVX7-1
	C1orf141	NM_001276352.2		c.-104+512G>A		intron	N/A	NP_001263281.1	F2Z2X7
	C1orf141	NR_075077.2		n.41+512G>A		intron	N/A

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.826 AC: 125714 AN: 152164 Hom.: 51947 Cov.: 34

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.784

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.826 AC: 125786 AN: 152282 Hom.: 51973 Cov.: 34 AF XY: 0.828 AC XY: 61642 AN XY: 74466

African (AFR) AF: 0.779 AC: 32351 AN: 41544

American (AMR) AF: 0.833 AC: 12735 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.784 AC: 2723 AN: 3472

East Asian (EAS) AF: 0.923 AC: 4785 AN: 5184

South Asian (SAS) AF: 0.910 AC: 4396 AN: 4830

European-Finnish (FIN) AF: 0.845 AC: 8966 AN: 10610

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57099 AN: 68028

Other (OTH) AF: 0.798 AC: 1685 AN: 2112

Alfa AF: 0.829 Hom.: 20498

Bravo AF: 0.823

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.73
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;