1-67135003-G-T

Variant names:

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

Variant summary

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

The ENST00000371007.6(C1orf141):​c.-103-3776C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 134,208 control chromosomes in the GnomAD database, including 4,527 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 0.25 (4521 hom., cov: 26)
  • Exomes 𝑓: 0.21 (6 hom.)
• 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

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>A		upstream_gene	N/A	NP_001263280.1	Q5JVX7-1
	C1orf141	NM_001276352.2		c.-177C>A		upstream_gene	N/A	NP_001263281.1	F2Z2X7
	C1orf141	NR_075077.2		n.-33C>A		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>A		intron	N/A	ENSP00000360046.1	Q5JVX7-1
	C1orf141	ENST00000448166.6	TSL:5	c.-103-3776C>A		intron	N/A	ENSP00000415519.2	Q5JVX6
	C1orf141	ENST00000684719.1	MANE Select	c.-177C>A		upstream_gene	N/A	ENSP00000507487.1	Q5JVX7-1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 32975 AN: 133978 Hom.: 4510 Cov.: 26

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.439

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.145

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.273

GnomAD4 exome AF: 0.209 AC: 31 AN: 148 Hom.: 6 Cov.: 0 AF XY: 0.202 AC XY: 17 AN XY: 84

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.217 AC: 30 AN: 138

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 1 AN: 10

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.246 AC: 33004 AN: 134060 Hom.: 4521 Cov.: 26 AF XY: 0.255 AC XY: 16389 AN XY: 64332

African (AFR) AF: 0.0949 AC: 3187 AN: 33596

American (AMR) AF: 0.439 AC: 5831 AN: 13270

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 502 AN: 3352

East Asian (EAS) AF: 0.331 AC: 1414 AN: 4278

South Asian (SAS) AF: 0.287 AC: 1138 AN: 3964

European-Finnish (FIN) AF: 0.389 AC: 3058 AN: 7854

Middle Eastern (MID) AF: 0.154 AC: 38 AN: 246

European-Non Finnish (NFE) AF: 0.265 AC: 17190 AN: 64802

Other (OTH) AF: 0.275 AC: 510 AN: 1852

Alfa AF: 0.242 Hom.: 1699

Bravo AF: 0.226

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.2
DANN	Benign	0.88
PhyloP100		-0.017
PromoterAI		-0.015	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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: rs12044149; hg19: chr1-67600686;