Variant 9-136672096-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2

The NM_016215.5(EGFL7):c.799+8C>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0049 in 1,545,936 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0035 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0051 ( 20 hom. )

Consequence

EGFL7
NM_016215.5 splice_region, intron

Scores

Splicing: ADA: 0.0008630

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.843

Variant links:

Genes affected

EGFL7 (HGNC:20594): (EGF like domain multiple 7) This gene encodes a secreted endothelial cell protein that contains two epidermal growth factor-like domains. The encoded protein may play a role in regulating vasculogenesis. This protein may be involved in the growth and proliferation of tumor cells. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Feb 2012]

EGFL7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.38).

BP6

Variant 9-136672096-C-A is Benign according to our data. Variant chr9-136672096-C-A is described in ClinVar as [Benign]. Clinvar id is 781671.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EGFL7	NM_016215.5 link	c.799+8C>A		splice_region_variant, intron_variant		ENST00000308874.12	NP_057299.1	Q9UHF1A0A024R8F5

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
EGFL7	ENST00000308874.12 link	c.799+8C>A	splice_region_variant, intron_variant	1	NM_016215.5	ENSP00000307843.7	Q9UHF1
EGFL7	ENST00000371698.3 link	c.799+8C>A	splice_region_variant, intron_variant	1		ENSP00000360763.3	Q9UHF1
EGFL7	ENST00000406555.7 link	c.799+8C>A	splice_region_variant, intron_variant	1		ENSP00000385639.3	Q9UHF1
EGFL7	ENST00000371699.5 link	c.799+8C>A	splice_region_variant, intron_variant	2		ENSP00000360764.1	Q9UHF1

Frequencies

GnomAD3 genomes

AF:

0.00354

AC:

539

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.0187

Gnomad AMR

AF:

0.00255

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00597

Gnomad OTH

AF:

0.00144

GnomAD3 exomes

AF:

0.00303

AC:

460

AN:

151740

Hom.:

AF XY:

0.00284

AC XY:

230

AN XY:

80994

show subpopulations

Gnomad AFR exome

AF:

0.00137

Gnomad AMR exome

AF:

0.00142

Gnomad ASJ exome

AF:

0.00226

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000444

Gnomad FIN exome

AF:

0.00178

Gnomad NFE exome

AF:

0.00587

Gnomad OTH exome

AF:

0.00328

GnomAD4 exome

AF:

0.00505

AC:

7042

AN:

1393640

Hom.:

Cov.:

AF XY:

0.00498

AC XY:

3423

AN XY:

687520

show subpopulations

Gnomad4 AFR exome

AF:

0.000758

Gnomad4 AMR exome

AF:

0.00196

Gnomad4 ASJ exome

AF:

0.00206

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000392

Gnomad4 FIN exome

AF:

0.00164

Gnomad4 NFE exome

AF:

0.00608

Gnomad4 OTH exome

AF:

0.00408

GnomAD4 genome

AF:

0.00354

AC:

539

AN:

152296

Hom.:

Cov.:

AF XY:

0.00322

AC XY:

240

AN XY:

74478

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.00255

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00597

Gnomad4 OTH

AF:

0.00142

Alfa

AF:

0.00361

Hom.:

Bravo

AF:

0.00405

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.38

CADD

Benign

5.5

DANN

Benign

0.93

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00086

dbscSNV1_RF

Benign

0.096

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