Variant chr4-5988779-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The ENST00000711657.1(C4orf50):c.3267C>T(p.Asn1089=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00309 in 1,536,058 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0021 ( 1 hom., cov: 32)

Exomes 𝑓: 0.0032 ( 6 hom. )

Consequence

C4orf50
ENST00000711657.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.13

Variant links:

Genes affected

C4orf50 (HGNC:33766): (chromosome 4 open reading frame 50)

C4orf50 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 4-5988779-G-A is Benign according to our data. Variant chr4-5988779-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2654615.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-1.13 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C4orf50	NM_001364689.3 linkuse as main transcript	c.3267C>T	p.Asn1089=	synonymous_variant	6/12	ENST00000711657.1
C4orf50	XM_017008893.2 linkuse as main transcript	c.2730C>T	p.Asn910=	synonymous_variant	5/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
C4orf50	ENST00000711657.1 linkuse as main transcript	c.3267C>T	p.Asn1089=	synonymous_variant	6/12		NM_001364689.3	P1
C4orf50	ENST00000531445.3 linkuse as main transcript	c.3267C>T	p.Asn1089=	synonymous_variant	28/34	5		P1
C4orf50	ENST00000639345.1 linkuse as main transcript	c.1287C>T	p.Asn429=	synonymous_variant, NMD_transcript_variant	1/8	5

Frequencies

GnomAD3 genomes

AF:

0.00210

AC:

319

AN:

152114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00101

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00203

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000850

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00338

Gnomad OTH

AF:

0.00192

GnomAD3 exomes

AF:

0.00178

AC:

240

AN:

134626

Hom.:

AF XY:

0.00170

AC XY:

125

AN XY:

73314

show subpopulations

Gnomad AFR exome

AF:

0.000620

Gnomad AMR exome

AF:

0.000858

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000952

Gnomad SAS exome

AF:

0.000267

Gnomad FIN exome

AF:

0.00111

Gnomad NFE exome

AF:

0.00369

Gnomad OTH exome

AF:

0.00169

GnomAD4 exome

AF:

0.00320

AC:

4428

AN:

1383826

Hom.:

Cov.:

AF XY:

0.00308

AC XY:

2106

AN XY:

682854

show subpopulations

Gnomad4 AFR exome

AF:

0.000791

Gnomad4 AMR exome

AF:

0.00109

Gnomad4 ASJ exome

AF:

0.000159

Gnomad4 EAS exome

AF:

0.0000280

Gnomad4 SAS exome

AF:

0.000164

Gnomad4 FIN exome

AF:

0.000944

Gnomad4 NFE exome

AF:

0.00386

Gnomad4 OTH exome

AF:

0.00264

GnomAD4 genome

AF:

0.00210

AC:

319

AN:

152232

Hom.:

Cov.:

AF XY:

0.00183

AC XY:

136

AN XY:

74422

show subpopulations

Gnomad4 AFR

AF:

0.00101

Gnomad4 AMR

AF:

0.00203

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.000850

Gnomad4 NFE

AF:

0.00338

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00110

Hom.:

Bravo

AF:

0.00212

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

CeGaT Center for Human Genetics Tuebingen

Sep 01, 2022

C4orf50: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.062

DANN

Benign

0.55

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