rs6687776

Variant names:

• chr1-1095185-C-T
• rs6687776
• NM_017891.5:c.-135-3082G>A

Variant summary

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

The NM_017891.5(C1orf159):​c.-135-3082G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,096 control chromosomes in the GnomAD database, including 7,191 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 0.27 (7191 hom., cov: 33)
• Consequence: C1orf159 NM_017891.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 16 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C1orf159	NM_017891.5	c.-135-3082G>A		intron_variant	Intron 1 of 9	ENST00000421241.7	NP_060361.4
C1orf159	NM_001330306.2	c.-135-3082G>A		intron_variant	Intron 2 of 11		NP_001317235.1
C1orf159	NM_001363525.2	c.-135-3082G>A		intron_variant	Intron 2 of 10		NP_001350454.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C1orf159	ENST00000421241.7	c.-135-3082G>A		intron_variant	Intron 1 of 9	2	NM_017891.5	ENSP00000400736.2

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40948 AN: 151978 Hom.: 7186 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.260

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

GnomAD4 genome AF: 0.269 AC: 40988 AN: 152096 Hom.: 7191 Cov.: 33 AF XY: 0.270 AC XY: 20051 AN XY: 74376

African (AFR) AF: 0.506 AC: 20953 AN: 41436

American (AMR) AF: 0.209 AC: 3194 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 701 AN: 3468

East Asian (EAS) AF: 0.188 AC: 972 AN: 5184

South Asian (SAS) AF: 0.233 AC: 1124 AN: 4824

European-Finnish (FIN) AF: 0.219 AC: 2317 AN: 10592

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11001 AN: 67996

Other (OTH) AF: 0.258 AC: 543 AN: 2106

Alfa AF: 0.205 Hom.: 11792

Bravo AF: 0.279

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.61
PhyloP100		0.36
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: rs6687776; hg19: chr1-1030565;