1-11778042-A-G

Position:

• chr1-11778042-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010881.2(C1orf167):​c.2340-618A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,854 control chromosomes in the GnomAD database, including 35,629 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 0.68 (35599 hom., cov: 29)
  • Exomes 𝑓: 0.73 (30 hom.)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

C1orf167 (HGNC:25262): (chromosome 1 open reading frame 167) Implicated in coronary artery disease. [provided by Alliance of Genome Resources, Apr 2022]

C1orf167-AS1 (HGNC:41091): (C1orf167 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf167	NM_001010881.2	c.2340-618A>G		intron_variant		ENST00000688073.1	NP_001010881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf167	ENST00000688073.1	c.2340-618A>G		intron_variant			NM_001010881.2	ENSP00000510540.1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102685 AN: 151636 Hom.: 35586 Cov.: 29

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.665

GnomAD4 exome AF: 0.730 AC: 73 AN: 100 Hom.: 30 Cov.: 0 AF XY: 0.743 AC XY: 55 AN XY: 74

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.750

Gnomad4 NFE exome AF: 0.795

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.677 AC: 102744 AN: 151754 Hom.: 35599 Cov.: 29 AF XY: 0.681 AC XY: 50520 AN XY: 74146

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.663

Alfa AF: 0.683 Hom.: 4835

Bravo AF: 0.670

Asia WGS AF: 0.742 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.83

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: rs10864540; hg19: chr1-11838099;