rs12134663

chr1-11778589-A-Cchr1-11778589-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.2340-71A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,193,464 control chromosomes in the GnomAD database, including 16,231 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 0.12 (1499 hom., cov: 33)
  • Exomes 𝑓: 0.16 (14732 hom.)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf167	NM_001010881.2	c.2340-71A>C		intron_variant		ENST00000688073.1
C1orf167-AS1	NR_126000.1	n.660+56T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf167	ENST00000688073.1	c.2340-71A>C		intron_variant			NM_001010881.2	A2
C1orf167-AS1	ENST00000376620.3	n.660+56T>G		intron_variant, non_coding_transcript_variant		1
C1orf167	ENST00000312793.9	c.490-71A>C		intron_variant		2
C1orf167	ENST00000433342.6	c.1854-71A>C		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18994 AN: 152092 Hom.: 1503 Cov.: 33

Gnomad AFR AF: 0.0310

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.164 AC: 170912 AN: 1041254 Hom.: 14732 AF XY: 0.167 AC XY: 83831 AN XY: 501382

Gnomad4 AFR exome AF: 0.0225

Gnomad4 AMR exome AF: 0.0784

Gnomad4 ASJ exome AF: 0.232

Gnomad4 EAS exome AF: 0.102

Gnomad4 SAS exome AF: 0.249

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.165

GnomAD4 genome AF: 0.125 AC: 18989 AN: 152210 Hom.: 1499 Cov.: 33 AF XY: 0.126 AC XY: 9348 AN XY: 74422

Gnomad4 AFR AF: 0.0309

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.145

Alfa AF: 0.0504 Hom.: 63

Bravo AF: 0.115

Asia WGS AF: 0.163 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.59
Dann	Benign	0.57

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: rs12134663; hg19: chr1-11838646;