dbSNP rs3130617: C6orf47:p.Gly68Arg (chr6-31659746-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021184.4(C6orf47):c.202G>A(p.Gly68Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 1,612,754 control chromosomes in the GnomAD database, including 456,605 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.75 ( 42636 hom., cov: 32)

Exomes 𝑓: 0.75 ( 413969 hom. )

Consequence

C6orf47
NM_021184.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.360

Publications

73 publications found

Variant links:

Genes affected

C6orf47 (HGNC:19076): (chromosome 6 open reading frame 47)

C6orf47 links:

C6orf47-AS1 (HGNC:39767): (C6orf47 antisense RNA 1)

C6orf47-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=1.1138699E-6).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf47	NM_021184.4 link	c.202G>A	p.Gly68Arg	missense_variant	Exon 1 of 1	ENST00000375911.2	NP_067007.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf47	ENST00000375911.2 link	c.202G>A	p.Gly68Arg	missense_variant	Exon 1 of 1	6	NM_021184.4	ENSP00000365076.1		O95873
C6orf47-AS1	ENST00000422049.1 link	n.352-654C>T		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes

AF:

0.746

AC:

113310

AN:

151956

Hom.:

42607

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.847

Gnomad AMR

AF:

0.771

Gnomad ASJ

AF:

0.884

Gnomad EAS

AF:

0.973

Gnomad SAS

AF:

0.840

Gnomad FIN

AF:

0.815

Gnomad MID

AF:

0.851

Gnomad NFE

AF:

0.740

Gnomad OTH

AF:

0.762

GnomAD2 exomes

AF:

0.794

AC:

195632

AN:

246376

AF XY:

0.793

show subpopulations

Gnomad AFR exome

AF:

0.674

Gnomad AMR exome

AF:

0.851

Gnomad ASJ exome

AF:

0.894

Gnomad EAS exome

AF:

0.980

Gnomad FIN exome

AF:

0.802

Gnomad NFE exome

AF:

0.748

Gnomad OTH exome

AF:

0.782

GnomAD4 exome

AF:

0.750

AC:

1095381

AN:

1460680

Hom.:

413969

Cov.:

AF XY:

0.752

AC XY:

546719

AN XY:

726644

show subpopulations

African (AFR)

AF:

0.672

AC:

22513

AN:

33478

American (AMR)

AF:

0.843

AC:

37702

AN:

44718

Ashkenazi Jewish (ASJ)

AF:

0.890

AC:

23268

AN:

26132

East Asian (EAS)

AF:

0.982

AC:

39001

AN:

39700

South Asian (SAS)

AF:

0.810

AC:

69893

AN:

86254

European-Finnish (FIN)

AF:

0.795

AC:

41596

AN:

52298

Middle Eastern (MID)

AF:

0.816

AC:

4708

AN:

5768

European-Non Finnish (NFE)

AF:

0.729

AC:

810715

AN:

1111950

Other (OTH)

AF:

0.762

AC:

45985

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

19444

38889

58333

77778

97222

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

20038

40076

60114

80152

100190

<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:

0.746

AC:

113386

AN:

152074

Hom.:

42636

Cov.:

AF XY:

0.752

AC XY:

55935

AN XY:

74354

show subpopulations

African (AFR)

AF:

0.672

AC:

27838

AN:

41424

American (AMR)

AF:

0.772

AC:

11805

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.884

AC:

3068

AN:

3472

East Asian (EAS)

AF:

0.973

AC:

5038

AN:

5178

South Asian (SAS)

AF:

0.839

AC:

4050

AN:

4826

European-Finnish (FIN)

AF:

0.815

AC:

8640

AN:

10598

Middle Eastern (MID)

AF:

0.854

AC:

251

AN:

294

European-Non Finnish (NFE)

AF:

0.740

AC:

50307

AN:

67964

Other (OTH)

AF:

0.766

AC:

1620

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1451

2902

4354

5805

7256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

850

1700

2550

3400

4250

<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:

0.762

Hom.:

117503

Bravo

AF:

0.740

TwinsUK

AF:

0.730

AC:

2705

ALSPAC

AF:

0.720

AC:

2775

ESP6500AA

AF:

0.689

AC:

2081

ESP6500EA

AF:

0.743

AC:

4028

ExAC

AF:

0.788

AC:

92193

Asia WGS

AF:

0.905

AC:

3146

AN:

3478

EpiCase

AF:

0.767

EpiControl

AF:

0.770

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.064

BayesDel_addAF

Benign

-0.82

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.5

(source)

DANN

Benign

0.53

DEOGEN2

Benign

0.0022

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.4

FATHMM_MKL

Benign

0.019

LIST_S2

Benign

0.27

MetaRNN

Benign

0.0000011

MetaSVM

Benign

-0.97

MutationAssessor

Benign

0.26

PhyloP100

-0.36

PROVEAN

Benign

-0.80

REVEL

Benign

0.028

Sift

Benign

0.87

Sift4G

Benign

0.14

Polyphen

0.0

Vest4

0.0080

MutPred

0.11

Gain of MoRF binding (P = 0.0084);

MPC

0.34

ClinPred

0.011

GERP RS

-0.64

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.058

gMVP

0.0079

Mutation Taster

=100/0

polymorphism (auto)

(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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over