Variant chrX-13600045-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_015507.4(EGFL6):c.351G>A(p.Lys117=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00477 in 1,209,514 control chromosomes in the GnomAD database, including 131 homozygotes. There are 1,574 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.022 ( 65 hom., 689 hem., cov: 22)

Exomes 𝑓: 0.0030 ( 66 hom. 885 hem. )

Consequence

EGFL6
NM_015507.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.82

Variant links:

Genes affected

EGFL6 (HGNC:3235): (EGF like domain multiple 6) This gene encodes a member of the epidermal growth factor (EGF) repeat superfamily. Members of this superfamily are characterized by the presence of EGF-like repeats and are often involved in the regulation of cell cycle, proliferation, and developmental processes. The gene product contains a signal peptide, suggesting that it is secreted; an EGF repeat region consisting of 4 complete EGF-like repeats and 1 partial EGF-like repeat, 3 of which have a calcium-binding consensus sequence; an arg-gly-asp integrin association motif; and a MAM domain, which is believed to have an adhesive function. This gene is expressed early during development, and its expression has been detected in lung and meningioma tumors. [provided by RefSeq, Jul 2008]

EGFL6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

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

BP6

Variant X-13600045-G-A is Benign according to our data. Variant chrX-13600045-G-A is described in ClinVar as [Benign]. Clinvar id is 780682.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.82 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EGFL6	NM_015507.4 linkuse as main transcript	c.351G>A	p.Lys117=	synonymous_variant	4/12	ENST00000361306.6
EGFL6	NM_001167890.2 linkuse as main transcript	c.351G>A	p.Lys117=	synonymous_variant	4/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EGFL6	ENST00000361306.6 linkuse as main transcript	c.351G>A	p.Lys117=	synonymous_variant	4/12	1	NM_015507.4	A2	Q8IUX8-1
EGFL6	ENST00000380602.3 linkuse as main transcript	c.351G>A	p.Lys117=	synonymous_variant	4/12	1		P4	Q8IUX8-2

Frequencies

GnomAD3 genomes

AF:

0.0223

AC:

2493

AN:

111724

Hom.:

Cov.:

AF XY:

0.0200

AC XY:

678

AN XY:

33886

show subpopulations

Gnomad AFR

AF:

0.0756

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0100

Gnomad ASJ

AF:

0.000377

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000371

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0169

Gnomad NFE

AF:

0.000696

Gnomad OTH

AF:

0.0180

GnomAD3 exomes

AF:

0.00735

AC:

1344

AN:

182950

Hom.:

AF XY:

0.00466

AC XY:

314

AN XY:

67444

show subpopulations

Gnomad AFR exome

AF:

0.0796

Gnomad AMR exome

AF:

0.00762

Gnomad ASJ exome

AF:

0.00107

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000263

Gnomad FIN exome

AF:

0.0000627

Gnomad NFE exome

AF:

0.000831

Gnomad OTH exome

AF:

0.00310

GnomAD4 exome

AF:

0.00297

AC:

3257

AN:

1097739

Hom.:

Cov.:

AF XY:

0.00244

AC XY:

885

AN XY:

363155

show subpopulations

Gnomad4 AFR exome

AF:

0.0776

Gnomad4 AMR exome

AF:

0.00836

Gnomad4 ASJ exome

AF:

0.00103

Gnomad4 EAS exome

AF:

0.0000331

Gnomad4 SAS exome

AF:

0.000333

Gnomad4 FIN exome

AF:

0.0000494

Gnomad4 NFE exome

AF:

0.000627

Gnomad4 OTH exome

AF:

0.00695

GnomAD4 genome

AF:

0.0224

AC:

2509

AN:

111775

Hom.:

Cov.:

AF XY:

0.0203

AC XY:

689

AN XY:

33947

show subpopulations

Gnomad4 AFR

AF:

0.0759

Gnomad4 AMR

AF:

0.00990

Gnomad4 ASJ

AF:

0.000377

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000744

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000696

Gnomad4 OTH

AF:

0.0178

Alfa

AF:

0.0129

Hom.:

Bravo

AF:

0.0265

EpiCase

AF:

0.00115

EpiControl

AF:

0.00131

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Apr 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

6.5

DANN

Benign

0.75

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