1-11775878-T-C

Variant names:

• chr1-11775878-T-C
• rs6696752
• NM_001010881.2:c.2164+268T>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.2164+268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,064 control chromosomes in the GnomAD database, including 35,644 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 0.68 (35644 hom., cov: 32)
• Consequence: C1orf167 NM_001010881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 12 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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.2164+268T>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.2164+268T>C		intron	N/A	ENSP00000510540.1	Q5SNV9-1
	C1orf167	ENST00000433342.6	TSL:5	c.1678+268T>C		intron	N/A	ENSP00000414909.3	A0AAG2QDU5
	C1orf167	ENST00000312793.9	TSL:2	c.313+268T>C		intron	N/A	ENSP00000317749.5	H7BXQ2

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102847 AN: 151946 Hom.: 35632 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.677 AC: 102907 AN: 152064 Hom.: 35644 Cov.: 32 AF XY: 0.681 AC XY: 50639 AN XY: 74348

African (AFR) AF: 0.530 AC: 21953 AN: 41444

American (AMR) AF: 0.777 AC: 11866 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2282 AN: 3468

East Asian (EAS) AF: 0.888 AC: 4590 AN: 5170

South Asian (SAS) AF: 0.663 AC: 3197 AN: 4824

European-Finnish (FIN) AF: 0.784 AC: 8298 AN: 10586

Middle Eastern (MID) AF: 0.572 AC: 167 AN: 292

European-Non Finnish (NFE) AF: 0.714 AC: 48542 AN: 67980

Other (OTH) AF: 0.664 AC: 1404 AN: 2114

Alfa AF: 0.694 Hom.: 18944

Bravo AF: 0.670

Asia WGS AF: 0.743 AC: 2584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs6696752; hg19: chr1-11835935;