dbSNP rs3756814: C6orf62:c.*530A>G (chr6-24705607-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_030939.5(C6orf62):c.*530A>G variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.328 in 152,612 control chromosomes in the GnomAD database, including 8,625 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.33 ( 8593 hom., cov: 33)

Exomes 𝑓: 0.38 ( 32 hom. )

Consequence

C6orf62
NM_030939.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.07

Publications

14 publications found

Variant links:

Genes affected

C6orf62 (HGNC:20998): (chromosome 6 open reading frame 62)

C6orf62 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.3).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.383 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf62	NM_030939.5 link	c.*530A>G		3_prime_UTR_variant	Exon 5 of 5	ENST00000378119.9	NP_112201.1	Q9GZU0-1A0A024R026
C6orf62	NM_001410835.1 link	c.*530A>G		3_prime_UTR_variant	Exon 5 of 5		NP_001397764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf62	ENST00000378119.9 link	c.*530A>G		3_prime_UTR_variant	Exon 5 of 5	1	NM_030939.5	ENSP00000367359.4		Q9GZU0-1
C6orf62	ENST00000710317.1 link	c.*530A>G		3_prime_UTR_variant	Exon 5 of 5			ENSP00000518198.1

Frequencies

GnomAD3 genomes

AF:

0.328

AC:

49837

AN:

152066

Hom.:

8595

Cov.:

show subpopulations

Gnomad AFR

AF:

0.230

Gnomad AMI

AF:

0.477

Gnomad AMR

AF:

0.304

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.387

Gnomad FIN

AF:

0.361

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.387

Gnomad OTH

AF:

0.316

GnomAD4 exome

AF:

0.376

AC:

161

AN:

428

Hom.:

Cov.:

AF XY:

0.366

AC XY:

AN XY:

262

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.371

AC:

156

AN:

420

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.750

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

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:

0.328

AC:

49847

AN:

152184

Hom.:

8593

Cov.:

AF XY:

0.324

AC XY:

24137

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.230

AC:

9570

AN:

41552

American (AMR)

AF:

0.304

AC:

4646

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.387

AC:

1343

AN:

3468

East Asian (EAS)

AF:

0.207

AC:

1075

AN:

5184

South Asian (SAS)

AF:

0.386

AC:

1863

AN:

4824

European-Finnish (FIN)

AF:

0.361

AC:

3815

AN:

10578

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.387

AC:

26315

AN:

67984

Other (OTH)

AF:

0.314

AC:

663

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1711

3422

5134

6845

8556

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

496

992

1488

1984

2480

<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:

0.363

Hom.:

9253

Bravo

AF:

0.319

Asia WGS

AF:

0.287

AC:

1000

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.30

CADD

Benign

(source)

DANN

Benign

0.92

PhyloP100

4.1

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