1-11778042-A-G

Variant names:

• chr1-11778042-A-G
• rs10864540
• ENST00000376620.3:n.903T>C

Variant summary

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

The ENST00000376620.3(C1orf167-AS1):​n.903T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,854 control chromosomes in the GnomAD database, including 35,629 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 (35599 hom., cov: 29)
  • Exomes 𝑓: 0.73 (30 hom.)
• Consequence: C1orf167-AS1 ENST00000376620.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870
• Publications: 7 publications found

Genes affected

C1orf167-AS1 (HGNC:41091): (C1orf167 antisense RNA 1)

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf167	NM_001010881.2	c.2340-618A>G		intron_variant	Intron 10 of 20	ENST00000688073.1	NP_001010881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf167	ENST00000688073.1	c.2340-618A>G		intron_variant	Intron 10 of 20		NM_001010881.2	ENSP00000510540.1

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102685 AN: 151636 Hom.: 35586 Cov.: 29

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.777

Gnomad ASJ AF: 0.657

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.665

GnomAD4 exome AF: 0.730 AC: 73 AN: 100 Hom.: 30 Cov.: 0 AF XY: 0.743 AC XY: 55 AN XY: 74

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 1.00 AC: 4 AN: 4

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.795 AC: 62 AN: 78

Other (OTH) AF: 0.250 AC: 3 AN: 12

GnomAD4 genome AF: 0.677 AC: 102744 AN: 151754 Hom.: 35599 Cov.: 29 AF XY: 0.681 AC XY: 50520 AN XY: 74146

African (AFR) AF: 0.531 AC: 21960 AN: 41360

American (AMR) AF: 0.777 AC: 11829 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.657 AC: 2280 AN: 3470

East Asian (EAS) AF: 0.887 AC: 4565 AN: 5146

South Asian (SAS) AF: 0.662 AC: 3193 AN: 4820

European-Finnish (FIN) AF: 0.784 AC: 8253 AN: 10530

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48493 AN: 67902

Other (OTH) AF: 0.663 AC: 1395 AN: 2104

Alfa AF: 0.676 Hom.: 4935

Bravo AF: 0.670

Asia WGS AF: 0.742 AC: 2582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.83
PhyloP100		-0.087
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: rs10864540; hg19: chr1-11838099;