dbSNP rs777942397: C8orf82:p.Gln50His (chr8-144528767-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001001795.2(C8orf82):c.150G>T(p.Gln50His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000283 in 1,413,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000013 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

C8orf82
NM_001001795.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.0780

Publications

1 publications found

Variant links:

Genes affected

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

C8orf82 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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=0.16790584).

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>T	p.Gln50His	missense	Exon 1 of 3	NP_001001795.1	Q6P1X6-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
C8orf82	ENST00000524821.6	TSL:1 MANE Select	c.150G>T	p.Gln50His	missense	Exon 1 of 3	ENSP00000436621.1	Q6P1X6-1
C8orf82	ENST00000313465.5	TSL:1	c.150G>T	p.Gln50His	missense	Exon 1 of 2	ENSP00000316262.5	J3KNI2
C8orf82	ENST00000527462.1	TSL:3	c.295G>T	p.Gly99Trp	missense	Exon 1 of 2	ENSP00000436060.1	H0YEK9

Frequencies

GnomAD3 genomes

AF:

0.0000133

AC:

AN:

150034

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000132

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

GnomAD2 exomes

AF:

0.0000235

AC:

AN:

84992

AF XY:

0.0000208

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000893

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000254

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000158

AC:

AN:

1263344

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

613832

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

24782

American (AMR)

AF:

0.0000496

AC:

AN:

20180

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18114

East Asian (EAS)

AF:

0.00

AC:

AN:

29340

South Asian (SAS)

AF:

0.00

AC:

AN:

57838

European-Finnish (FIN)

AF:

0.00

AC:

AN:

45100

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3976

European-Non Finnish (NFE)

AF:

9.87e-7

AC:

AN:

1012764

Other (OTH)

AF:

0.00

AC:

AN:

51250

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.550

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000133

AC:

AN:

150034

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

73252

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

40200

American (AMR)

AF:

0.000132

AC:

AN:

15136

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3454

East Asian (EAS)

AF:

0.00

AC:

AN:

5086

South Asian (SAS)

AF:

0.00

AC:

AN:

4780

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10474

Middle Eastern (MID)

AF:

0.00

AC:

AN:

314

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67624

Other (OTH)

AF:

0.00

AC:

AN:

2058

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.0000302

ExAC

AF:

0.0000431

AC:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.40

BayesDel_addAF

Benign

-0.0065

BayesDel_noAF

Benign

-0.25

CADD

Benign

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

Eigen

Benign

-0.036

Eigen_PC

Benign

-0.038

FATHMM_MKL

Benign

0.63

LIST_S2

Uncertain

0.92

M_CAP

Uncertain

0.11

MetaRNN

Benign

0.17

MetaSVM

Benign

-0.85

MutationAssessor

Benign

1.7

PhyloP100

0.078

PROVEAN

Uncertain

-4.2

REVEL

Benign

0.14

Sift

Benign

0.049

Sift4G

Uncertain

0.0080

Polyphen

1.0

Vest4

0.42

MutPred

0.31

Loss of sheet (P = 0.0357)

MVP

0.099

MPC

1.5

ClinPred

0.95

GERP RS

1.2

PromoterAI

0.040

Neutral

(source)

Varity_R

0.39

gMVP

0.72

Mutation Taster

=85/15

polymorphism

(source)

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over