rs1889292

Positions:

• chr1-11780886-T-C

Variant summary

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

The NM_001010881.2(C1orf167):​c.2860+876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 151,750 control chromosomes in the GnomAD database, including 25,318 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 0.57 (25318 hom., cov: 30)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf167	NM_001010881.2	c.2860+876T>C		intron_variant		ENST00000688073.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf167	ENST00000688073.1	c.2860+876T>C		intron_variant			NM_001010881.2	A2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85762 AN: 151632 Hom.: 25313 Cov.: 30

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.574

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.565 AC: 85796 AN: 151750 Hom.: 25318 Cov.: 30 AF XY: 0.569 AC XY: 42185 AN XY: 74156

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.767

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.573

Alfa AF: 0.585 Hom.: 3349

Bravo AF: 0.565

Asia WGS AF: 0.595 AC: 2069 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.6
DANN	Benign	0.60

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: rs1889292; hg19: chr1-11840943;