dbSNP rs13077498: C3orf62:p.Glu110Lys (chr3-49276545-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_198562.3(C3orf62):c.328G>A(p.Glu110Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 1,614,096 control chromosomes in the GnomAD database, including 8,566 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 0.093 ( 737 hom., cov: 32)

Exomes 𝑓: 0.10 ( 7829 hom. )

Consequence

C3orf62
NM_198562.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.27

Publications

37 publications found

Variant links:

Genes affected

C3orf62 (HGNC:24771): (chromosome 3 open reading frame 62)

C3orf62 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=0.0011317432).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C3orf62	NM_198562.3 link	c.328G>A	p.Glu110Lys	missense_variant	Exon 1 of 3	ENST00000343010.8	NP_940964.1	Q6ZUJ4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
C3orf62	ENST00000343010.8 link	c.328G>A	p.Glu110Lys	missense_variant	Exon 1 of 3	1	NM_198562.3	ENSP00000341139.3	Q6ZUJ4
C3orf62	ENST00000436325.1 link	c.322G>A	p.Glu108Lys	missense_variant	Exon 2 of 4	4		ENSP00000413663.1	C9JW57
C3orf62	ENST00000424960.1 link	n.267+31G>A		intron_variant	Intron 1 of 2	5		ENSP00000391945.1	H7BZX3

Frequencies

GnomAD3 genomes

AF:

0.0934

AC:

14200

AN:

152110

Hom.:

737

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0837

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.0759

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.0345

Gnomad SAS

AF:

0.0600

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.0981

Gnomad NFE

AF:

0.105

Gnomad OTH

AF:

0.0966

GnomAD2 exomes

AF:

0.0880

AC:

22127

AN:

251494

AF XY:

0.0873

show subpopulations

Gnomad AFR exome

AF:

0.0816

Gnomad AMR exome

AF:

0.0511

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.0344

Gnomad FIN exome

AF:

0.118

Gnomad NFE exome

AF:

0.108

Gnomad OTH exome

AF:

0.0963

GnomAD4 exome

AF:

0.101

AC:

147779

AN:

1461868

Hom.:

7829

Cov.:

AF XY:

0.0996

AC XY:

72423

AN XY:

727234

show subpopulations

African (AFR)

AF:

0.0817

AC:

2734

AN:

33480

American (AMR)

AF:

0.0544

AC:

2435

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

3208

AN:

26136

East Asian (EAS)

AF:

0.0403

AC:

1599

AN:

39700

South Asian (SAS)

AF:

0.0582

AC:

5018

AN:

86256

European-Finnish (FIN)

AF:

0.119

AC:

6375

AN:

53418

Middle Eastern (MID)

AF:

0.0810

AC:

467

AN:

5768

European-Non Finnish (NFE)

AF:

0.108

AC:

120178

AN:

1111994

Other (OTH)

AF:

0.0955

AC:

5765

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

8405

16810

25214

33619

42024

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0933

AC:

14201

AN:

152228

Hom.:

737

Cov.:

AF XY:

0.0927

AC XY:

6897

AN XY:

74416

show subpopulations

African (AFR)

AF:

0.0835

AC:

3466

AN:

41520

American (AMR)

AF:

0.0758

AC:

1159

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.126

AC:

439

AN:

3472

East Asian (EAS)

AF:

0.0347

AC:

180

AN:

5180

South Asian (SAS)

AF:

0.0601

AC:

290

AN:

4828

European-Finnish (FIN)

AF:

0.114

AC:

1210

AN:

10588

Middle Eastern (MID)

AF:

0.109

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.105

AC:

7144

AN:

68028

Other (OTH)

AF:

0.0956

AC:

202

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

680

1359

2039

2718

3398

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.101

Hom.:

2452

Bravo

AF:

0.0897

TwinsUK

AF:

0.115

AC:

427

ALSPAC

AF:

0.105

AC:

406

ESP6500AA

AF:

0.0872

AC:

384

ESP6500EA

AF:

0.108

AC:

932

ExAC

AF:

0.0882

AC:

10709

Asia WGS

AF:

0.0530

AC:

187

AN:

3478

EpiCase

AF:

0.109

EpiControl

AF:

0.110

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.067

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.51

CADD

Benign

0.18

(source)

DANN

Benign

0.87

DEOGEN2

Benign

0.0013

T;T

Eigen

Benign

-1.9

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.0088

LIST_S2

Benign

0.60

T;T

MetaRNN

Benign

0.0011

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

-0.90

N;.

PhyloP100

-1.3

PROVEAN

Benign

1.4

N;N

REVEL

Benign

0.094

Sift

Benign

1.0

T;T

Sift4G

Benign

1.0

T;.

Polyphen

0.0

B;.

Vest4

0.014

MPC

0.066

ClinPred

0.0067

GERP RS

-7.3

Varity_R

0.11

gMVP

0.065

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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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rs13077498

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