ENST00000371007.6:c.-103-3776C>G

Variant names:

• chr1-67135003-G-C
• rs12044149
• ENST00000371007.6:c.-103-3776C>G

Variant summary

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

The ENST00000371007.6(C1orf141):​c.-103-3776C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.000015 (0 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: C1orf141 ENST00000371007.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 27 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371007.6. 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.-177C>G		upstream_gene	N/A	NP_001263280.1	Q5JVX7-1
	C1orf141	NM_001276352.2		c.-177C>G		upstream_gene	N/A	NP_001263281.1	F2Z2X7
	C1orf141	NR_075077.2		n.-33C>G		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf141	ENST00000371007.6	TSL:5	c.-103-3776C>G		intron	N/A	ENSP00000360046.1	Q5JVX7-1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-3776C>G		intron	N/A	ENSP00000415519.2	Q5JVX6
	C1orf141	ENST00000684719.1	MANE Select	c.-177C>G		upstream_gene	N/A	ENSP00000507487.1	Q5JVX7-1

Frequencies

GnomAD3 genomes AF: 0.0000149 AC: 2 AN: 134136 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.0000298

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000127

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000149 AC: 2 AN: 134218 Hom.: 0 Cov.: 26 AF XY: 0.0000310 AC XY: 2 AN XY: 64420

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000298 AC: 1 AN: 33612

American (AMR) AF: 0.00 AC: 0 AN: 13296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3356

East Asian (EAS) AF: 0.00 AC: 0 AN: 4292

South Asian (SAS) AF: 0.00 AC: 0 AN: 3972

European-Finnish (FIN) AF: 0.000127 AC: 1 AN: 7872

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 246

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 64870

Other (OTH) AF: 0.00 AC: 0 AN: 1856

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 1699

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.67
PhyloP100		-0.017
PromoterAI		-0.028	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs12044149; hg19: chr1-67600686;