Genetic Variant NM_001164478.2:c.-7-6118A>G (chr5-127065120-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001164478.2(C5orf63):c.-7-6118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0205 in 152,306 control chromosomes in the GnomAD database, including 77 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 0.020 ( 77 hom., cov: 32)

Consequence

C5orf63
NM_001164478.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.792

Publications

0 publications found

Variant links:

Genes affected

C5orf63 (HGNC:40051): (chromosome 5 open reading frame 63)

C5orf63 links:

ENSG00000298097 (HGNC:):

ENSG00000298097 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 (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C5orf63	NM_001164478.2 link	c.-7-6118A>G		intron_variant	Intron 2 of 4	ENST00000296662.10	NP_001157950.1	A6NC05-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf63	ENST00000296662.10 link	c.-7-6118A>G		intron_variant	Intron 2 of 4	5	NM_001164478.2	ENSP00000453964.1		A6NC05-2

Frequencies

GnomAD3 genomes

AF:

0.0205

AC:

3122

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0118

Gnomad AMI

AF:

0.0208

Gnomad AMR

AF:

0.0128

Gnomad ASJ

AF:

0.0403

Gnomad EAS

AF:

0.0913

Gnomad SAS

AF:

0.116

Gnomad FIN

AF:

0.0297

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0128

Gnomad OTH

AF:

0.0177

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.0205

AC:

3116

AN:

152306

Hom.:

Cov.:

AF XY:

0.0232

AC XY:

1729

AN XY:

74484

show subpopulations

African (AFR)

AF:

0.0118

AC:

489

AN:

41578

American (AMR)

AF:

0.0127

AC:

195

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0403

AC:

140

AN:

3470

East Asian (EAS)

AF:

0.0912

AC:

472

AN:

5178

South Asian (SAS)

AF:

0.117

AC:

562

AN:

4818

European-Finnish (FIN)

AF:

0.0297

AC:

315

AN:

10622

Middle Eastern (MID)

AF:

0.0714

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0128

AC:

868

AN:

68022

Other (OTH)

AF:

0.0165

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

156

311

467

622

778

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0133

Hom.:

Bravo

AF:

0.0170

Asia WGS

AF:

0.0710

AC:

245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

6.2

(source)

DANN

Benign

0.76

PhyloP100

0.79

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over