Variant 1-11764246-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.885

Variant links:

Genes affected

C1orf167 (HGNC:25262): (chromosome 1 open reading frame 167) Implicated in coronary artery disease. [provided by Alliance of Genome Resources, Apr 2022]

C1orf167 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf167	NM_001010881.2 link	c.-70-85T>C		intron_variant		ENST00000688073.1	NP_001010881.1	Q5SNV9A2VCK6A0A8I5KXP5Q8NDG0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf167	ENST00000688073.1 link	c.-70-85T>C		intron_variant			NM_001010881.2	ENSP00000510540.1		A0A8I5KXP5
C1orf167	ENST00000433342.6 link	c.-70-85T>C		intron_variant		5		ENSP00000414909.3		Q5SNV9

Frequencies

GnomAD3 genomes

AF:

0.597

AC:

90713

AN:

151868

Hom.:

28348

Cov.:

show subpopulations

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

show subpopulations

Gnomad4 AFR exome

AF:

0.423

Gnomad4 AMR exome

AF:

0.795

Gnomad4 ASJ exome

AF:

0.637

Gnomad4 EAS exome

AF:

0.809

Gnomad4 SAS exome

AF:

0.459

Gnomad4 FIN exome

AF:

0.635

Gnomad4 NFE exome

AF:

0.672

Gnomad4 OTH exome

AF:

0.640

GnomAD4 genome

AF:

0.597

AC:

90750

AN:

151986

Hom.:

28351

Cov.:

AF XY:

0.597

AC XY:

44330

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.418

Gnomad4 AMR

AF:

0.738

Gnomad4 ASJ

AF:

0.637

Gnomad4 EAS

AF:

0.805

Gnomad4 SAS

AF:

0.475

Gnomad4 FIN

AF:

0.621

Gnomad4 NFE

AF:

0.661

Gnomad4 OTH

AF:

0.597

Alfa

AF:

0.652

Hom.:

41383

Bravo

AF:

0.601

Asia WGS

AF:

0.635

AC:

2210

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.4

DANN

Benign

0.87

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over