1-1096160-A-G

Variant names:

• chr1-1096160-A-G
• rs9651273
• NM_017891.5:c.-135-4057T>C

Variant summary

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

The NM_017891.5(C1orf159):​c.-135-4057T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.812 in 152,156 control chromosomes in the GnomAD database, including 50,908 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 0.81 (50908 hom., cov: 32)
• Consequence: C1orf159 NM_017891.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35
• Publications: 6 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017891.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf159	NM_017891.5	MANE Select	c.-135-4057T>C		intron	N/A	NP_060361.4
	C1orf159	NM_001330306.2		c.-135-4057T>C		intron	N/A	NP_001317235.1
	C1orf159	NM_001363525.2		c.-135-4057T>C		intron	N/A	NP_001350454.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf159	ENST00000421241.7	TSL:2 MANE Select	c.-135-4057T>C		intron	N/A	ENSP00000400736.2
	C1orf159	ENST00000379339.5	TSL:2	c.-135-4057T>C		intron	N/A	ENSP00000368644.1
	C1orf159	ENST00000434641.5	TSL:5	c.-135-4057T>C		intron	N/A	ENSP00000390635.1

Frequencies

GnomAD3 genomes AF: 0.812 AC: 123396 AN: 152038 Hom.: 50844 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.844

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.847

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.812 AC: 123525 AN: 152156 Hom.: 50908 Cov.: 32 AF XY: 0.816 AC XY: 60670 AN XY: 74382

African (AFR) AF: 0.933 AC: 38746 AN: 41516

American (AMR) AF: 0.844 AC: 12898 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2767 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5069 AN: 5180

South Asian (SAS) AF: 0.847 AC: 4077 AN: 4814

European-Finnish (FIN) AF: 0.757 AC: 8006 AN: 10578

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49383 AN: 67990

Other (OTH) AF: 0.807 AC: 1706 AN: 2114

Alfa AF: 0.766 Hom.: 94010

Bravo AF: 0.824

Asia WGS AF: 0.930 AC: 3233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.52
DANN	Benign	0.91
PhyloP100		-2.3
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: rs9651273; hg19: chr1-1031540;