rs3737728

Variant names:

• chr1-1086035-A-C
• rs3737728
• NM_017891.5:c.311-23T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-1086035-A-C
• chr1-1086035-A-G
• chr1-1086035-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_017891.5(C1orf159):​c.311-23T>G variant causes a intron 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. Variant has been reported in ClinVar as (no stars).

• Frequency: Genomes: not found (cov: 36)
• Consequence: C1orf159 NM_017891.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 15 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 -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

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.311-23T>G		intron	N/A	NP_060361.4
	C1orf159	NM_001330306.2		c.419-23T>G		intron	N/A	NP_001317235.1
	C1orf159	NM_001363525.2		c.311-23T>G		intron	N/A	NP_001350454.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf159	ENST00000421241.7	TSL:2 MANE Select	c.311-23T>G		intron	N/A	ENSP00000400736.2
	C1orf159	ENST00000379339.5	TSL:2	c.419-23T>G		intron	N/A	ENSP00000368644.1
	C1orf159	ENST00000379320.5	TSL:2	c.311-23T>G		intron	N/A	ENSP00000368624.1

Frequencies

GnomAD3 genomes Cov.: 36

GnomAD4 exome Cov.: 51

GnomAD4 genome Cov.: 36

Alfa AF: 0.00 Hom.: 61217

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.2
DANN	Benign	0.34
PhyloP100		-1.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3737728; hg19: chr1-1021415;