Genetic Variant EGFL6:p.Ile175Thr (chrX-13606382-T-C) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_015507.4(EGFL6):c.524T>C(p.Ile175Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000456 in 1,097,092 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 0.0000046 ( 0 hom. 2 hem. )

Consequence

EGFL6
NM_015507.4 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.66

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 Likely_benign. Variant got -4 ACMG points.

BS2

High Hemizygotes in GnomAdExome4 at 2 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EGFL6	NM_015507.4 link	c.524T>C	p.Ile175Thr	missense_variant	Exon 6 of 12	ENST00000361306.6	NP_056322.2	Q8IUX8-1
EGFL6	NM_001167890.2 link	c.524T>C	p.Ile175Thr	missense_variant	Exon 6 of 12		NP_001161362.1	Q8IUX8-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EGFL6	ENST00000361306.6 link	c.524T>C	p.Ile175Thr	missense_variant	Exon 6 of 12	1	NM_015507.4	ENSP00000355126.1		Q8IUX8-1
EGFL6	ENST00000380602.3 link	c.524T>C	p.Ile175Thr	missense_variant	Exon 6 of 12	1		ENSP00000369976.3		Q8IUX8-2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000549

AC:

AN:

182237

Hom.:

AF XY:

0.0000150

AC XY:

AN XY:

66741

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000724

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000456

AC:

AN:

1097092

Hom.:

Cov.:

AF XY:

0.00000552

AC XY:

AN XY:

362520

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000663

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000356

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000113

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Dec 01, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.524T>C (p.I175T) alteration is located in exon 6 (coding exon 6) of the EGFL6 gene. This alteration results from a T to C substitution at nucleotide position 524, causing the isoleucine (I) at amino acid position 175 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.069

BayesDel_addAF

Benign

-0.092

BayesDel_noAF

Benign

-0.18

CADD

Benign

DANN

Uncertain

0.97

DEOGEN2

Benign

0.37

T;.

FATHMM_MKL

Uncertain

0.84

LIST_S2

Benign

0.84

T;T

M_CAP

Benign

0.053

MetaRNN

Uncertain

0.46

T;T

MetaSVM

Uncertain

-0.24

MutationAssessor

Benign

2.0

M;M

PrimateAI

Benign

0.43

PROVEAN

Uncertain

-4.1

D;D

REVEL

Uncertain

0.42

Sift

Uncertain

0.020

D;D

Sift4G

Uncertain

0.0020

D;D

Polyphen

0.15

B;B

Vest4

0.38

MutPred

0.79

Loss of stability (P = 0.0131);Loss of stability (P = 0.0131);

MVP

0.37

MPC

0.33

ClinPred

0.41

GERP RS

4.0

Varity_R

0.42

gMVP

0.95

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