dbSNP rs941900: EVL:c.965-516C>A (chr14-100137062-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016337.3(EVL):c.965-516C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 159,166 control chromosomes in the GnomAD database, including 51,042 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.80 ( 49404 hom., cov: 33)

Exomes 𝑓: 0.67 ( 1638 hom. )

Consequence

EVL
NM_016337.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.907

Publications

6 publications found

Variant links:

Genes affected

EVL (HGNC:20234): (Enah/Vasp-like) Predicted to enable SH3 domain binding activity and profilin binding activity. Involved in negative regulation of epithelial cell migration; negative regulation of ruffle assembly; and positive regulation of stress fiber assembly. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

EVL links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016337.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EVL	NM_016337.3	MANE Select	c.965-516C>A		intron	N/A	NP_057421.1	Q9UI08-2
	EVL	NM_001330221.2		c.959-516C>A		intron	N/A	NP_001317150.1	Q9UI08-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EVL	ENST00000392920.8	TSL:1 MANE Select	c.965-516C>A	intron	N/A	ENSP00000376652.3	Q9UI08-2
EVL	ENST00000402714.6	TSL:1	c.959-516C>A	intron	N/A	ENSP00000384720.2	Q9UI08-1
EVL	ENST00000873444.1		c.1229-516C>A	intron	N/A	ENSP00000543503.1

Frequencies

GnomAD3 genomes

AF:

0.803

AC:

122064

AN:

152052

Hom.:

49353

Cov.:

show subpopulations

Gnomad AFR

AF:

0.903

Gnomad AMI

AF:

0.833

Gnomad AMR

AF:

0.795

Gnomad ASJ

AF:

0.727

Gnomad EAS

AF:

0.820

Gnomad SAS

AF:

0.765

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.690

Gnomad NFE

AF:

0.749

Gnomad OTH

AF:

0.767

GnomAD4 exome

AF:

0.674

AC:

4712

AN:

6996

Hom.:

1638

Cov.:

AF XY:

0.672

AC XY:

2450

AN XY:

3648

show subpopulations

African (AFR)

AF:

0.764

AC:

AN:

106

American (AMR)

AF:

0.749

AC:

1330

AN:

1776

Ashkenazi Jewish (ASJ)

AF:

0.613

AC:

AN:

East Asian (EAS)

AF:

0.680

AC:

283

AN:

416

South Asian (SAS)

AF:

0.625

AC:

440

AN:

704

European-Finnish (FIN)

AF:

0.417

AC:

AN:

Middle Eastern (MID)

AF:

0.333

AC:

AN:

European-Non Finnish (NFE)

AF:

0.647

AC:

2341

AN:

3618

Other (OTH)

AF:

0.677

AC:

180

AN:

266

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

126

190

253

316

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

144

216

288

360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.803

AC:

122174

AN:

152170

Hom.:

49404

Cov.:

AF XY:

0.807

AC XY:

60003

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.903

AC:

37509

AN:

41530

American (AMR)

AF:

0.795

AC:

12168

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.727

AC:

2524

AN:

3472

East Asian (EAS)

AF:

0.820

AC:

4232

AN:

5158

South Asian (SAS)

AF:

0.764

AC:

3680

AN:

4818

European-Finnish (FIN)

AF:

0.809

AC:

8562

AN:

10584

Middle Eastern (MID)

AF:

0.684

AC:

201

AN:

294

European-Non Finnish (NFE)

AF:

0.749

AC:

50931

AN:

68006

Other (OTH)

AF:

0.766

AC:

1609

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1237

2473

3710

4946

6183

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

872

1744

2616

3488

4360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.762

Hom.:

124897

Bravo

AF:

0.805

Asia WGS

AF:

0.818

AC:

2843

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.14

(source)

DANN

Benign

0.44

PhyloP100

-0.91

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over