rs4845881

Variant names:

• chr1-11768262-G-A
• rs4845881
• NM_001010881.2:c.1529G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-11768262-G-A
• chr1-11768262-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010881.2(C1orf167):​c.1529G>A​(p.Arg510Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 1,289,670 control chromosomes in the GnomAD database, including 278,410 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.62 (30381 hom., cov: 33)
  • Exomes 𝑓: 0.66 (248029 hom.)
• Consequence: C1orf167 NM_001010881.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 24 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 (MetaRNN=1.215919E-6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf167	NM_001010881.2	MANE Select	c.1529G>A	p.Arg510Gln	missense	Exon 5 of 21	NP_001010881.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf167	ENST00000688073.1	MANE Select	c.1529G>A	p.Arg510Gln	missense	Exon 5 of 21	ENSP00000510540.1
	C1orf167	ENST00000433342.6	TSL:5	c.1154G>A	p.Arg385Gln	missense	Exon 6 of 21	ENSP00000414909.3
	C1orf167	ENST00000484153.1	TSL:2	n.574G>A		non_coding_transcript_exon	Exon 3 of 9

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94762 AN: 151988 Hom.: 30381 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.611

GnomAD2 exomes AF: 0.658 AC: 89864 AN: 136472 AF XY: 0.645

Gnomad AFR exome AF: 0.469

Gnomad AMR exome AF: 0.794

Gnomad ASJ exome AF: 0.631

Gnomad EAS exome AF: 0.739

Gnomad FIN exome AF: 0.731

Gnomad NFE exome AF: 0.667

Gnomad OTH exome AF: 0.656

GnomAD4 exome AF: 0.657 AC: 747817 AN: 1137564 Hom.: 248029 Cov.: 59 AF XY: 0.651 AC XY: 363527 AN XY: 558074

African (AFR) AF: 0.477 AC: 11649 AN: 24412

American (AMR) AF: 0.791 AC: 22354 AN: 28258

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 10160 AN: 15934

East Asian (EAS) AF: 0.744 AC: 9550 AN: 12832

South Asian (SAS) AF: 0.496 AC: 37778 AN: 76198

European-Finnish (FIN) AF: 0.731 AC: 9655 AN: 13214

Middle Eastern (MID) AF: 0.562 AC: 2472 AN: 4398

European-Non Finnish (NFE) AF: 0.671 AC: 617454 AN: 920784

Other (OTH) AF: 0.644 AC: 26745 AN: 41534

GnomAD4 genome AF: 0.623 AC: 94799 AN: 152106 Hom.: 30381 Cov.: 33 AF XY: 0.628 AC XY: 46698 AN XY: 74350

African (AFR) AF: 0.477 AC: 19764 AN: 41460

American (AMR) AF: 0.729 AC: 11151 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2213 AN: 3470

East Asian (EAS) AF: 0.740 AC: 3820 AN: 5162

South Asian (SAS) AF: 0.506 AC: 2440 AN: 4818

European-Finnish (FIN) AF: 0.738 AC: 7820 AN: 10592

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45521 AN: 67990

Other (OTH) AF: 0.609 AC: 1288 AN: 2116

Alfa AF: 0.651 Hom.: 129395

Bravo AF: 0.619

TwinsUK AF: 0.670 AC: 2486

ALSPAC AF: 0.674 AC: 2599

ExAC AF: 0.540 AC: 10948

Asia WGS AF: 0.620 AC: 2158 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.096
BayesDel_addAF	Benign	-0.78	T
BayesDel_noAF	Benign	-0.75
CADD	Benign	12
DANN	Benign	0.84
DEOGEN2	Benign	0.00061	T
Eigen	Benign	-0.57
Eigen_PC	Benign	-0.69
FATHMM_MKL	Benign	0.077	N
LIST_S2	Benign	0.42	T
MetaRNN	Benign	0.0000012	T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.26	N
PhyloP100		-0.037
PROVEAN	Benign	0.15	N
REVEL	Benign	0.033
Sift	Benign	0.37	T
Sift4G	Benign	0.45	T
Vest4		0.032
MPC		0.39
ClinPred		0.0056	T
GERP RS		-1.4
Varity_R		0.042
gMVP		0.079
Mutation Taster		=96/4	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: rs4845881; hg19: chr1-11828319; COSMIC: COSV107359266; COSMIC: COSV107359266;