1-11780886-T-C

Variant names:

• chr1-11780886-T-C
• rs1889292
• NM_001010881.2:c.2860+876T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
C1orf167	NM_001010881.2	c.2860+876T>C		intron_variant	Intron 13 of 20	ENST00000688073.1	NP_001010881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf167	ENST00000688073.1	c.2860+876T>C		intron_variant	Intron 13 of 20		NM_001010881.2	ENSP00000510540.1

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

African (AFR) AF: 0.398 AC: 16448 AN: 41316

American (AMR) AF: 0.705 AC: 10741 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3468

East Asian (EAS) AF: 0.767 AC: 3957 AN: 5156

South Asian (SAS) AF: 0.470 AC: 2264 AN: 4818

European-Finnish (FIN) AF: 0.657 AC: 6905 AN: 10516

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41408 AN: 67930

Other (OTH) AF: 0.573 AC: 1207 AN: 2106

Alfa AF: 0.576 Hom.: 3405

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
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1889292; hg19: chr1-11840943;