Variant 21-32412920-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1

The NM_058187.5(EVA1C):c.67C>A(p.Arg23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00319 in 1,526,036 control chromosomes in the GnomAD database, including 139 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0051 ( 12 hom., cov: 33)

Exomes 𝑓: 0.0030 ( 127 hom. )

Consequence

EVA1C
NM_058187.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.287

Variant links:

Genes affected

EVA1C (HGNC:13239): (eva-1 homolog C) Enables heparin binding activity. Colocalizes with extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

EVA1C links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 21-32412920-C-A is Benign according to our data. Variant chr21-32412920-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 2848841.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.287 with no splicing effect.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVA1C	NM_058187.5 linkuse as main transcript	c.67C>A	p.Arg23=	synonymous_variant	1/8	ENST00000300255.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVA1C	ENST00000300255.7 linkuse as main transcript	c.67C>A	p.Arg23=	synonymous_variant	1/8	1	NM_058187.5	P3	P58658-1

Frequencies

GnomAD3 genomes

AF:

0.00510

AC:

777

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00135

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0285

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0341

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00546

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000559

Gnomad OTH

AF:

0.00334

GnomAD3 exomes

AF:

0.0106

AC:

1363

AN:

128130

Hom.:

AF XY:

0.00807

AC XY:

571

AN XY:

70736

show subpopulations

Gnomad AFR exome

AF:

0.00137

Gnomad AMR exome

AF:

0.0485

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0262

Gnomad SAS exome

AF:

0.000821

Gnomad FIN exome

AF:

0.00390

Gnomad NFE exome

AF:

0.000458

Gnomad OTH exome

AF:

0.00711

GnomAD4 exome

AF:

0.00298

AC:

4100

AN:

1373698

Hom.:

127

Cov.:

AF XY:

0.00278

AC XY:

1883

AN XY:

678366

show subpopulations

Gnomad4 AFR exome

AF:

0.000595

Gnomad4 AMR exome

AF:

0.0474

Gnomad4 ASJ exome

AF:

0.0000409

Gnomad4 EAS exome

AF:

0.0568

Gnomad4 SAS exome

AF:

0.000831

Gnomad4 FIN exome

AF:

0.00360

Gnomad4 NFE exome

AF:

0.000191

Gnomad4 OTH exome

AF:

0.00400

GnomAD4 genome

AF:

0.00507

AC:

773

AN:

152338

Hom.:

Cov.:

AF XY:

0.00549

AC XY:

409

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00135

Gnomad4 AMR

AF:

0.0282

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.0342

Gnomad4 SAS

AF:

0.000827

Gnomad4 FIN

AF:

0.00546

Gnomad4 NFE

AF:

0.000559

Gnomad4 OTH

AF:

0.00331

Alfa

AF:

0.00113

Hom.:

Bravo

AF:

0.00727

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 22, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

7.0

DANN

Benign

0.91

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over