chr1-1086035-A-G

Position:

• chr1-1086035-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017891.5(C1orf159):​c.311-23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 1,610,786 control chromosomes in the GnomAD database, including 438,884 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 0.76 (43689 hom., cov: 36)
  • Exomes 𝑓: 0.73 (395195 hom.)
• Consequence: C1orf159 NM_017891.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

C1orf159 (HGNC:26062): (chromosome 1 open reading frame 159) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

C1orf159 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C1orf159	NM_017891.5	c.311-23T>C		intron_variant		ENST00000421241.7	NP_060361.4
C1orf159	NM_001330306.2	c.419-23T>C		intron_variant			NP_001317235.1
C1orf159	NM_001363525.2	c.311-23T>C		intron_variant			NP_001350454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C1orf159	ENST00000421241.7	c.311-23T>C		intron_variant		2	NM_017891.5	ENSP00000400736.2

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114937 AN: 152172 Hom.: 43652 Cov.: 36

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.811

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.767

GnomAD3 exomes AF: 0.762 AC: 188000 AN: 246568 Hom.: 72085 AF XY: 0.760 AC XY: 101769 AN XY: 133890

Gnomad AFR exome AF: 0.786

Gnomad AMR exome AF: 0.823

Gnomad ASJ exome AF: 0.797

Gnomad EAS exome AF: 0.895

Gnomad SAS exome AF: 0.785

Gnomad FIN exome AF: 0.730

Gnomad NFE exome AF: 0.716

Gnomad OTH exome AF: 0.756

GnomAD4 exome AF: 0.735 AC: 1071693 AN: 1458496 Hom.: 395195 Cov.: 51 AF XY: 0.736 AC XY: 533574 AN XY: 725396

Gnomad4 AFR exome AF: 0.780

Gnomad4 AMR exome AF: 0.821

Gnomad4 ASJ exome AF: 0.797

Gnomad4 EAS exome AF: 0.910

Gnomad4 SAS exome AF: 0.781

Gnomad4 FIN exome AF: 0.729

Gnomad4 NFE exome AF: 0.718

Gnomad4 OTH exome AF: 0.748

GnomAD4 genome AF: 0.755 AC: 115038 AN: 152290 Hom.: 43689 Cov.: 36 AF XY: 0.759 AC XY: 56506 AN XY: 74462

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.811

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.768

Alfa AF: 0.726 Hom.: 47714

Bravo AF: 0.760

Asia WGS AF: 0.840 AC: 2922 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.33

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

Other links and lift over

dbSNP: rs3737728; hg19: chr1-1021415; COSMIC: COSV53881166; COSMIC: COSV53881166;