1-11764246-T-C

Variant names:

• chr1-11764246-T-C
• rs4845877
• NM_001010881.2:c.-70-85T>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.-70-85T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 507,088 control chromosomes in the GnomAD database, including 103,094 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 0.60 (28351 hom., cov: 32)
  • Exomes 𝑓: 0.64 (74743 hom.)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.885
• Publications: 14 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010881.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf167	NM_001010881.2	MANE Select	c.-70-85T>C		intron	N/A	NP_001010881.1	Q5SNV9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf167	ENST00000688073.1	MANE Select	c.-70-85T>C		intron	N/A	ENSP00000510540.1	Q5SNV9-1
	C1orf167	ENST00000433342.6	TSL:5	c.-70-85T>C		intron	N/A	ENSP00000414909.3	A0AAG2QDU5

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90713 AN: 151868 Hom.: 28348 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.598

GnomAD4 exome AF: 0.640 AC: 227342 AN: 355102 Hom.: 74743 AF XY: 0.624 AC XY: 118214 AN XY: 189364

African (AFR) AF: 0.423 AC: 3949 AN: 9336

American (AMR) AF: 0.795 AC: 18844 AN: 23710

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 5243 AN: 8236

East Asian (EAS) AF: 0.809 AC: 7237 AN: 8944

South Asian (SAS) AF: 0.459 AC: 24926 AN: 54336

European-Finnish (FIN) AF: 0.635 AC: 6696 AN: 10552

Middle Eastern (MID) AF: 0.567 AC: 1537 AN: 2710

European-Non Finnish (NFE) AF: 0.672 AC: 149053 AN: 221868

Other (OTH) AF: 0.640 AC: 9857 AN: 15410

GnomAD4 genome AF: 0.597 AC: 90750 AN: 151986 Hom.: 28351 Cov.: 32 AF XY: 0.597 AC XY: 44330 AN XY: 74292

African (AFR) AF: 0.418 AC: 17311 AN: 41420

American (AMR) AF: 0.738 AC: 11280 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2210 AN: 3470

East Asian (EAS) AF: 0.805 AC: 4152 AN: 5156

South Asian (SAS) AF: 0.475 AC: 2290 AN: 4824

European-Finnish (FIN) AF: 0.621 AC: 6560 AN: 10562

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.661 AC: 44910 AN: 67954

Other (OTH) AF: 0.597 AC: 1260 AN: 2112

Alfa AF: 0.640 Hom.: 106704

Bravo AF: 0.601

Asia WGS AF: 0.635 AC: 2210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.87
PhyloP100		-0.89
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: rs4845877; hg19: chr1-11824303;