1-67135003-G-T

Position:

• chr1-67135003-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf141	NM_001276351.2			upstream_gene_variant		ENST00000684719.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf141	ENST00000684719.1			upstream_gene_variant			NM_001276351.2	P1

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

Gnomad4 EAS exome AF: 0.217

Gnomad4 NFE exome AF: 0.100

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

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.331

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.275

Alfa AF: 0.239 Hom.: 992

Bravo AF: 0.226

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.2
DANN	Benign	0.88

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

Publications

LitVar

Other links and lift over

dbSNP: rs12044149; hg19: chr1-67600686;