Genetic Variant NM_001001795.2:c.511G>A (chr8-144527482-C-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate

The NM_001001795.2(C8orf82):c.511G>A(p.Ala171Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000716 in 1,256,782 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 34)

Exomes 𝑓: 0.000074 ( 0 hom. )

Consequence

C8orf82
NM_001001795.2 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.692

Publications

0 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: 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 (MetaRNN=0.14167345).

BP6

Variant 8-144527482-C-T is Benign according to our data. Variant chr8-144527482-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2391115.Status of the report is criteria_provided_single_submitter, 1 stars.

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.511G>A	p.Ala171Thr	missense	Exon 3 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.511G>A	p.Ala171Thr	missense	Exon 3 of 3	ENSP00000436621.1	Q6P1X6-1
C8orf82	ENST00000313465.5	TSL:1	c.*486G>A		3_prime_UTR	Exon 2 of 2	ENSP00000316262.5	J3KNI2
C8orf82	ENST00000532827.1	TSL:2	c.643G>A	p.Ala215Thr	missense	Exon 3 of 3	ENSP00000437092.1	H0YF29

Frequencies

GnomAD3 genomes

AF:

0.0000532

AC:

AN:

150288

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000485

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000132

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000445

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.00

AC:

AN:

1190

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000741

AC:

AN:

1106386

Hom.:

Cov.:

AF XY:

0.0000735

AC XY:

AN XY:

530878

show subpopulations

African (AFR)

AF:

0.0000469

AC:

AN:

21300

American (AMR)

AF:

0.00

AC:

AN:

7246

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13150

East Asian (EAS)

AF:

0.00

AC:

AN:

21260

South Asian (SAS)

AF:

0.0000756

AC:

AN:

39700

European-Finnish (FIN)

AF:

0.00

AC:

AN:

25322

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2878

European-Non Finnish (NFE)

AF:

0.0000794

AC:

AN:

932088

Other (OTH)

AF:

0.0000921

AC:

AN:

43442

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.535

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:

0.0000532

AC:

AN:

150396

Hom.:

Cov.:

AF XY:

0.0000681

AC XY:

AN XY:

73470

show subpopulations

African (AFR)

AF:

0.0000484

AC:

AN:

41360

American (AMR)

AF:

0.000132

AC:

AN:

15122

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3450

East Asian (EAS)

AF:

0.00

AC:

AN:

5144

South Asian (SAS)

AF:

0.000207

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9862

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0000445

AC:

AN:

67344

Other (OTH)

AF:

0.00

AC:

AN:

2090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

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:

0.0000378

ExAC

AF:

0.000168

AC:

ClinVar

ClinVar submissions

Significance:Likely benign

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

Benign

0.11

BayesDel_addAF

Benign

-0.061

BayesDel_noAF

Benign

-0.33

CADD

Benign

(source)

DANN

Benign

0.97

DEOGEN2

Benign

0.026

Eigen

Benign

-0.51

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.086

M_CAP

Pathogenic

0.44

MetaRNN

Benign

0.14

MetaSVM

Benign

-0.85

MutationAssessor

Uncertain

2.3

PhyloP100

0.69

PROVEAN

Benign

-0.50

REVEL

Benign

0.032

Sift

Benign

0.41

Sift4G

Benign

0.38

Polyphen

0.032

Vest4

0.098

MutPred

0.35

Loss of helix (P = 0.0093)

MVP

0.030

MPC

0.93

ClinPred

0.36

GERP RS

0.47

PromoterAI

-0.036

Neutral

(source)

Varity_R

0.034

gMVP

0.39

Mutation Taster

=96/4

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

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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