chr1-1113575-A-G

Position:

• chr1-1113575-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.-136+2485T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 152,208 control chromosomes in the GnomAD database, including 720 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 0.085 (720 hom., cov: 32)
• Consequence: C1orf159 NM_017891.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.164 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C1orf159	NM_017891.5	c.-136+2485T>C		intron_variant		ENST00000421241.7
C1orf159	NM_001330306.2	c.-136+1447T>C		intron_variant
C1orf159	NM_001363525.2	c.-136+1447T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C1orf159	ENST00000421241.7	c.-136+2485T>C		intron_variant		2	NM_017891.5	P1

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12926 AN: 152090 Hom.: 722 Cov.: 32

Gnomad AFR AF: 0.0224

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.0849 AC: 12916 AN: 152208 Hom.: 720 Cov.: 32 AF XY: 0.0836 AC XY: 6221 AN XY: 74418

Gnomad4 AFR AF: 0.0223

Gnomad4 AMR AF: 0.114

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0435

Gnomad4 NFE AF: 0.104

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0953 Hom.: 402

Bravo AF: 0.0881

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.8
DANN	Benign	0.47

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: rs4970405; hg19: chr1-1048955;