Variant rs12978500 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_001136263.2(C2CD4C):c.*162G>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 0.688 in 546,802 control chromosomes in the GnomAD database, including 131,840 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 0.68 ( 35267 hom., cov: 32)

Exomes 𝑓: 0.69 ( 96573 hom. )

Consequence

C2CD4C
NM_001136263.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Variant links:

Genes affected

C2CD4C (HGNC:29417): (C2 calcium dependent domain containing 4C) Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

C2CD4C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C2CD4C	NM_001136263.2 linkuse as main transcript	c.*162G>T		3_prime_UTR_variant	2/2	ENST00000332235.8	NP_001129735.1
C2CD4C	XM_011527694.2 linkuse as main transcript	c.1179+249G>T		intron_variant			XP_011525996.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C2CD4C	ENST00000332235.8 linkuse as main transcript	c.*162G>T		3_prime_UTR_variant	2/2	2	NM_001136263.2	ENSP00000328677	P1

Frequencies

GnomAD3 genomes

AF:

0.678

AC:

102743

AN:

151628

Hom.:

35253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.578

Gnomad AMI

AF:

0.796

Gnomad AMR

AF:

0.736

Gnomad ASJ

AF:

0.639

Gnomad EAS

AF:

0.814

Gnomad SAS

AF:

0.746

Gnomad FIN

AF:

0.665

Gnomad MID

AF:

0.642

Gnomad NFE

AF:

0.712

Gnomad OTH

AF:

0.692

GnomAD4 exome

AF:

0.692

AC:

273464

AN:

395056

Hom.:

96573

Cov.:

AF XY:

0.694

AC XY:

143076

AN XY:

206212

show subpopulations

Gnomad4 AFR exome

AF:

0.553

Gnomad4 AMR exome

AF:

0.739

Gnomad4 ASJ exome

AF:

0.618

Gnomad4 EAS exome

AF:

0.816

Gnomad4 SAS exome

AF:

0.715

Gnomad4 FIN exome

AF:

0.638

Gnomad4 NFE exome

AF:

0.690

Gnomad4 OTH exome

AF:

0.678

GnomAD4 genome

AF:

0.677

AC:

102804

AN:

151746

Hom.:

35267

Cov.:

AF XY:

0.678

AC XY:

50311

AN XY:

74192

show subpopulations

Gnomad4 AFR

AF:

0.578

Gnomad4 AMR

AF:

0.736

Gnomad4 ASJ

AF:

0.639

Gnomad4 EAS

AF:

0.814

Gnomad4 SAS

AF:

0.745

Gnomad4 FIN

AF:

0.665

Gnomad4 NFE

AF:

0.712

Gnomad4 OTH

AF:

0.694

Alfa

AF:

0.704

Hom.:

35946

Bravo

AF:

0.678

Asia WGS

AF:

0.777

AC:

2702

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.7

DANN

Benign

0.68

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

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