chr1-51123983-G-T

Variant names:

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

Variant summary

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

The NM_001136508.2(C1orf185):​c.258+5182G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 150,572 control chromosomes in the GnomAD database, including 37,653 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 0.68 (37653 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

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>T		intron	N/A	NP_001129980.1	Q5T7R7
	C1orf185	NM_001410790.1		c.258+5182G>T		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>T		intron	N/A	ENSP00000360824.2	Q5T7R7
	C1orf185	ENST00000467127.5	TSL:3	c.75+5182G>T		intron	N/A	ENSP00000473351.1	R4GMU4
	C1orf185	ENST00000648827.1		c.258+5182G>T		intron	N/A	ENSP00000497349.1	A0A3B3ISR6

Frequencies

GnomAD3 genomes AF: 0.683 AC: 102806 AN: 150466 Hom.: 37666 Cov.: 29

Gnomad AFR AF: 0.384

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.760

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.683 AC: 102801 AN: 150572 Hom.: 37653 Cov.: 29 AF XY: 0.689 AC XY: 50675 AN XY: 73524

African (AFR) AF: 0.383 AC: 15740 AN: 41046

American (AMR) AF: 0.801 AC: 12067 AN: 15068

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2620 AN: 3462

East Asian (EAS) AF: 0.754 AC: 3899 AN: 5170

South Asian (SAS) AF: 0.759 AC: 3633 AN: 4784

European-Finnish (FIN) AF: 0.837 AC: 8479 AN: 10134

Middle Eastern (MID) AF: 0.741 AC: 215 AN: 290

European-Non Finnish (NFE) AF: 0.796 AC: 53868 AN: 67638

Other (OTH) AF: 0.713 AC: 1484 AN: 2080

Alfa AF: 0.762 Hom.: 55242

Bravo AF: 0.670

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.14
DANN	Benign	0.13
PhyloP100		0.25
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: rs6588399; hg19: chr1-51589655; COSMIC: COSV65624294;