NM_017891.5:c.357T>A

Variant names:

• chr1-1085966-A-T
• NM_017891.5:c.357T>A
• C1orf159 p.Ile119Ile

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_017891.5(C1orf159):​c.357T>A​(p.Ile119Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: C1orf159 NM_017891.5 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.85
• Publications: 0 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BP7: Synonymous conserved (PhyloP=2.85 with no splicing effect.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf159	NM_017891.5	MANE Select	c.357T>A	p.Ile119Ile	synonymous	Exon 7 of 10	NP_060361.4
	C1orf159	NM_001330306.2		c.465T>A	p.Ile155Ile	synonymous	Exon 9 of 12	NP_001317235.1	Q96HA4-1
	C1orf159	NM_001363525.2		c.357T>A	p.Ile119Ile	synonymous	Exon 8 of 11	NP_001350454.1	Q5T2W9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf159	ENST00000421241.7	TSL:2 MANE Select	c.357T>A	p.Ile119Ile	synonymous	Exon 7 of 10	ENSP00000400736.2	Q96HA4-4
	C1orf159	ENST00000379339.5	TSL:2	c.465T>A	p.Ile155Ile	synonymous	Exon 9 of 12	ENSP00000368644.1	Q96HA4-1
	C1orf159	ENST00000379320.5	TSL:2	c.357T>A	p.Ile119Ile	synonymous	Exon 5 of 8	ENSP00000368624.1	Q5T2W9

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		2.8
Mutation Taster		=100/0	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-1021346;