14-100117612-G-A

Variant names:

• chr14-100117612-G-A
• rs2181102
• NM_016337.3:c.359-5927G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016337.3(EVL):​c.359-5927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,220 control chromosomes in the GnomAD database, including 49,533 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 (49533 hom., cov: 33)
• Consequence: EVL NM_016337.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277
• Publications: 3 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EVL	NM_016337.3	c.359-5927G>A		intron_variant	Intron 3 of 13	ENST00000392920.8	NP_057421.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EVL	ENST00000392920.8	c.359-5927G>A		intron_variant	Intron 3 of 13	1	NM_016337.3	ENSP00000376652.3

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122281 AN: 152102 Hom.: 49482 Cov.: 33

Gnomad AFR AF: 0.899

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.766

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.804 AC: 122390 AN: 152220 Hom.: 49533 Cov.: 33 AF XY: 0.809 AC XY: 60186 AN XY: 74416

African (AFR) AF: 0.900 AC: 37366 AN: 41534

American (AMR) AF: 0.797 AC: 12177 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2506 AN: 3472

East Asian (EAS) AF: 0.823 AC: 4258 AN: 5172

South Asian (SAS) AF: 0.768 AC: 3706 AN: 4824

European-Finnish (FIN) AF: 0.829 AC: 8779 AN: 10596

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.750 AC: 51020 AN: 68016

Other (OTH) AF: 0.765 AC: 1617 AN: 2114

Alfa AF: 0.783 Hom.: 18400

Bravo AF: 0.805

Asia WGS AF: 0.820 AC: 2853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.64
PhyloP100		-0.28
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2181102; hg19: chr14-100583949;