chr1-67134418-C-T

Position:

• chr1-67134418-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf141	NM_001276351.2	c.-104+512G>A		intron_variant		ENST00000684719.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf141	ENST00000684719.1	c.-104+512G>A		intron_variant			NM_001276351.2	P1

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

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.784

Gnomad4 EAS AF: 0.923

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.798

Alfa AF: 0.824 Hom.: 11459

Bravo AF: 0.823

Asia WGS AF: 0.915 AC: 3182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.73

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

Publications

LitVar

Other links and lift over

dbSNP: rs12069782; hg19: chr1-67600101;