Genetic Variant ENST00000470503.1:c.*58G>T (chr2-75702112-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000470503.1(GCFC2):c.*58G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 1,517,722 control chromosomes in the GnomAD database, including 139,030 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 0.50 ( 20462 hom., cov: 32)

Exomes 𝑓: 0.41 ( 118568 hom. )

Consequence

GCFC2
ENST00000470503.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116

Publications

10 publications found

Variant links:

Genes affected

GCFC2 (HGNC:1317): (GC-rich sequence DNA-binding factor 2) The first mRNA transcript isolated for this gene was part of an artificial chimera derived from two distinct gene transcripts and a primer used in the cloning process (see Genbank accession M29204). A positively charged amino terminus present only in the chimera was determined to bind GC-rich DNA, thus mistakenly thought to identify a transcription factor gene. [provided by RefSeq, Jul 2008]

GCFC2 links:

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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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GCFC2	NM_003203.5 link	c.619+87G>T		intron_variant	Intron 3 of 16	ENST00000321027.8	NP_003194.3	P16383-1A4UHR0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GCFC2	ENST00000321027.8 link	c.619+87G>T		intron_variant	Intron 3 of 16	1	NM_003203.5	ENSP00000318690.3		P16383-1

Frequencies

GnomAD3 genomes

AF:

0.499

AC:

75742

AN:

151856

Hom.:

20425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.730

Gnomad AMI

AF:

0.294

Gnomad AMR

AF:

0.437

Gnomad ASJ

AF:

0.304

Gnomad EAS

AF:

0.380

Gnomad SAS

AF:

0.420

Gnomad FIN

AF:

0.477

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.405

Gnomad OTH

AF:

0.429

GnomAD4 exome

AF:

0.412

AC:

562138

AN:

1365748

Hom.:

118568

Cov.:

AF XY:

0.409

AC XY:

277144

AN XY:

676910

show subpopulations

African (AFR)

AF:

0.743

AC:

22296

AN:

30012

American (AMR)

AF:

0.492

AC:

19236

AN:

39092

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

7166

AN:

23604

East Asian (EAS)

AF:

0.347

AC:

12570

AN:

36236

South Asian (SAS)

AF:

0.400

AC:

30112

AN:

75300

European-Finnish (FIN)

AF:

0.457

AC:

16935

AN:

37092

Middle Eastern (MID)

AF:

0.296

AC:

1174

AN:

3970

European-Non Finnish (NFE)

AF:

0.404

AC:

429633

AN:

1063574

Other (OTH)

AF:

0.405

AC:

23016

AN:

56868

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

14809

29618

44427

59236

74045

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.499

AC:

75830

AN:

151974

Hom.:

20462

Cov.:

AF XY:

0.497

AC XY:

36907

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.730

AC:

30300

AN:

41484

American (AMR)

AF:

0.438

AC:

6678

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.304

AC:

1053

AN:

3468

East Asian (EAS)

AF:

0.380

AC:

1967

AN:

5172

South Asian (SAS)

AF:

0.418

AC:

2013

AN:

4816

European-Finnish (FIN)

AF:

0.477

AC:

5017

AN:

10522

Middle Eastern (MID)

AF:

0.323

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.405

AC:

27545

AN:

67936

Other (OTH)

AF:

0.424

AC:

894

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1873

3747

5620

7494

9367

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.491

Hom.:

3501

Bravo

AF:

0.508

Asia WGS

AF:

0.422

AC:

1473

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.80

(source)

DANN

Benign

0.42

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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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ENST00000470503.1:c.*58G>T

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