1-11776991-C-G

Position:

• chr1-11776991-C-G

Variant summary

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

The NM_001010881.2(C1orf167):​c.2339+353C>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 154,792 control chromosomes in the GnomAD database, including 36,322 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 (35439 hom., cov: 34)
  • Exomes 𝑓: 0.75 (883 hom.)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• 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.2339+353C>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.2339+353C>G		intron_variant			NM_001010881.2	ENSP00000510540	A2
C1orf167	ENST00000312793.9	c.489+353C>G		intron_variant		2		ENSP00000317749
C1orf167	ENST00000433342.6	c.1853+353C>G		intron_variant		5		ENSP00000414909	P4
C1orf167	ENST00000484153.1	n.1385-138C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.676 AC: 102472 AN: 151586 Hom.: 35427 Cov.: 34

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.667

GnomAD4 exome AF: 0.751 AC: 2321 AN: 3090 Hom.: 883 AF XY: 0.752 AC XY: 1226 AN XY: 1630

Gnomad4 AFR exome AF: 0.600

Gnomad4 AMR exome AF: 0.847

Gnomad4 ASJ exome AF: 0.579

Gnomad4 EAS exome AF: 0.900

Gnomad4 SAS exome AF: 0.660

Gnomad4 FIN exome AF: 0.712

Gnomad4 NFE exome AF: 0.735

Gnomad4 OTH exome AF: 0.765

GnomAD4 genome AF: 0.676 AC: 102531 AN: 151702 Hom.: 35439 Cov.: 34 AF XY: 0.680 AC XY: 50410 AN XY: 74120

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.776

Gnomad4 ASJ AF: 0.657

Gnomad4 EAS AF: 0.887

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.665

Alfa AF: 0.617 Hom.: 2070

Bravo AF: 0.670

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.16

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: rs4846040; hg19: chr1-11837048;