Variant rs3088180 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001201335.2(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
NM_001201335.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.116

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:

GCFC2 (HGNC:):

GCFC2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GCFC2	NM_003203.5 linkuse as main transcript	c.619+87G>T		intron_variant		ENST00000321027.8	NP_003194.3	P16383-1A4UHR0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GCFC2	ENST00000321027.8 linkuse as main transcript	c.619+87G>T		intron_variant		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

Gnomad4 AFR exome

AF:

0.743

Gnomad4 AMR exome

AF:

0.492

Gnomad4 ASJ exome

AF:

0.304

Gnomad4 EAS exome

AF:

0.347

Gnomad4 SAS exome

AF:

0.400

Gnomad4 FIN exome

AF:

0.457

Gnomad4 NFE exome

AF:

0.404

Gnomad4 OTH exome

AF:

0.405

GnomAD4 genome

AF:

0.499

AC:

75830

AN:

151974

Hom.:

20462

Cov.:

AF XY:

0.497

AC XY:

36907

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.730

Gnomad4 AMR

AF:

0.438

Gnomad4 ASJ

AF:

0.304

Gnomad4 EAS

AF:

0.380

Gnomad4 SAS

AF:

0.418

Gnomad4 FIN

AF:

0.477

Gnomad4 NFE

AF:

0.405

Gnomad4 OTH

AF:

0.424

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

DANN

Benign

0.42

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over