8-144528767-C-G

Variant names:

• chr8-144528767-C-G
• rs777942397
• NM_001001795.2:c.150G>C

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001001795.2(C8orf82):​c.150G>C​(p.Gln50His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 150,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: 𝑓 0.000013 (0 hom., cov: 31)
• Consequence: C8orf82 NM_001001795.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

Genes affected

C8orf82 (HGNC:33826): (chromosome 8 open reading frame 82)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.25777406).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001001795.2. 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
	C8orf82	NM_001001795.2	MANE Select	c.150G>C	p.Gln50His	missense	Exon 1 of 3	NP_001001795.1	Q6P1X6-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C8orf82	ENST00000524821.6	TSL:1 MANE Select	c.150G>C	p.Gln50His	missense	Exon 1 of 3	ENSP00000436621.1	Q6P1X6-1
	C8orf82	ENST00000313465.5	TSL:1	c.150G>C	p.Gln50His	missense	Exon 1 of 2	ENSP00000316262.5	J3KNI2
	C8orf82	ENST00000527462.1	TSL:3	c.295G>C	p.Gly99Arg	missense	Exon 1 of 2	ENSP00000436060.1	H0YEK9

Frequencies

GnomAD3 genomes AF: 0.0000133 AC: 2 AN: 150034 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000498

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 35

GnomAD4 genome AF: 0.0000133 AC: 2 AN: 150034 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 73252

African (AFR) AF: 0.0000498 AC: 2 AN: 40200

American (AMR) AF: 0.00 AC: 0 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3454

East Asian (EAS) AF: 0.00 AC: 0 AN: 5086

South Asian (SAS) AF: 0.00 AC: 0 AN: 4780

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10474

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67624

Other (OTH) AF: 0.00 AC: 0 AN: 2058

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.40
BayesDel_addAF	Benign	-0.0065	T
BayesDel_noAF	Benign	-0.25
CADD	Benign	22
DANN	Uncertain	1.0
DEOGEN2	Benign	0.11	T
Eigen	Benign	-0.036
Eigen_PC	Benign	-0.038
FATHMM_MKL	Benign	0.65	D
LIST_S2	Uncertain	0.92	D
M_CAP	Uncertain	0.092	D
MetaRNN	Benign	0.26	T
MetaSVM	Benign	-0.85	T
MutationAssessor	Benign	1.7	L
PhyloP100		0.078
PROVEAN	Uncertain	-4.2	D
REVEL	Benign	0.15
Sift	Benign	0.049	D
Sift4G	Uncertain	0.0080	D
Polyphen		1.0	D
Vest4		0.42
MutPred		0.31		Loss of sheet (P = 0.0357)
MVP		0.099
MPC		1.5
ClinPred		0.99	D
GERP RS		1.2
PromoterAI		0.0093	Neutral
Varity_R		0.39
gMVP		0.72
Mutation Taster		=85/15	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

Other links and lift over

dbSNP: rs777942397; hg19: chr8-145754151;