rs6588399

Variant names:

• chr1-51123983-G-A
• rs6588399
• NM_001136508.2:c.258+5182G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-51123983-G-A
• chr1-51123983-G-T

Variant summary

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

The NM_001136508.2(C1orf185):​c.258+5182G>A 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: C1orf185 NM_001136508.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.248
• Publications: 2 publications found

Genes affected

C1orf185 (HGNC:28096): (chromosome 1 open reading frame 185) 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=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001136508.2. 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
	C1orf185	NM_001136508.2	MANE Select	c.258+5182G>A		intron	N/A	NP_001129980.1	Q5T7R7
	C1orf185	NM_001410790.1		c.258+5182G>A		intron	N/A	NP_001397719.1	A0A3B3ISR6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C1orf185	ENST00000371759.7	TSL:2 MANE Select	c.258+5182G>A		intron	N/A	ENSP00000360824.2	Q5T7R7
	C1orf185	ENST00000467127.5	TSL:3	c.75+5182G>A		intron	N/A	ENSP00000473351.1	R4GMU4
	C1orf185	ENST00000648827.1		c.258+5182G>A		intron	N/A	ENSP00000497349.1	A0A3B3ISR6

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 55242

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.17
DANN	Benign	0.20
PhyloP100		0.25

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: rs6588399; hg19: chr1-51589655;