chr1-67093186-CTCATT-C

Position:

• chr1-67093186-CTCATT-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_Strong BS2

The NM_001276351.2(C1orf141):​c.1017_1021del​(p.Met340CysfsTer7) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00911 in 1,613,812 control chromosomes in the GnomAD database, including 79 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0069 (8 hom., cov: 32)
  • Exomes 𝑓: 0.0093 (71 hom.)
• Consequence: C1orf141 NM_001276351.2 frameshift
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 2.13

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP6: Variant 1-67093186-CTCATT-C is Benign according to our data. Variant chr1-67093186-CTCATT-C is described in ClinVar as [Likely_benign]. Clinvar id is 778232.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS2: High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf141	NM_001276351.2	c.1017_1021del	p.Met340CysfsTer7	frameshift_variant	8/8	ENST00000684719.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf141	ENST00000684719.1	c.1017_1021del	p.Met340CysfsTer7	frameshift_variant	8/8		NM_001276351.2	P1

Frequencies

GnomAD3 genomes AF: 0.00686 AC: 1044 AN: 152086 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00196

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00845

Gnomad ASJ AF: 0.0228

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.000827

Gnomad FIN AF: 0.00368

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.00862

GnomAD3 exomes AF: 0.00603 AC: 1516 AN: 251282 Hom.: 11 AF XY: 0.00581 AC XY: 789 AN XY: 135800

Gnomad AFR exome AF: 0.00172

Gnomad AMR exome AF: 0.00335

Gnomad ASJ exome AF: 0.0229

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000490

Gnomad FIN exome AF: 0.00416

Gnomad NFE exome AF: 0.00871

Gnomad OTH exome AF: 0.00767

GnomAD4 exome AF: 0.00934 AC: 13656 AN: 1461608 Hom.: 71 AF XY: 0.00900 AC XY: 6544 AN XY: 727118

Gnomad4 AFR exome AF: 0.00158

Gnomad4 AMR exome AF: 0.00364

Gnomad4 ASJ exome AF: 0.0221

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000661

Gnomad4 FIN exome AF: 0.00502

Gnomad4 NFE exome AF: 0.0108

Gnomad4 OTH exome AF: 0.00838

GnomAD4 genome AF: 0.00686 AC: 1044 AN: 152204 Hom.: 8 Cov.: 32 AF XY: 0.00638 AC XY: 475 AN XY: 74422

Gnomad4 AFR AF: 0.00195

Gnomad4 AMR AF: 0.00843

Gnomad4 ASJ AF: 0.0228

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.000828

Gnomad4 FIN AF: 0.00368

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.00853

Alfa AF: 0.00785 Hom.: 2

Bravo AF: 0.00678

Asia WGS AF: 0.000289 AC: 1 AN: 3474

EpiCase AF: 0.0105

EpiControl AF: 0.0103

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Dec 01, 2022	C1orf141: BS2 -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 02, 2018	- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs200104842; hg19: chr1-67558869;