14-100120420-A-G

Position:

• chr14-100120420-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392920.8(EVL):​c.359-3119A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 152,210 control chromosomes in the GnomAD database, including 49,793 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 0.81 (49793 hom., cov: 32)
• Consequence: EVL ENST00000392920.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EVL	NM_016337.3	c.359-3119A>G		intron_variant		ENST00000392920.8	NP_057421.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EVL	ENST00000392920.8	c.359-3119A>G		intron_variant		1	NM_016337.3	ENSP00000376652	P1

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122580 AN: 152092 Hom.: 49741 Cov.: 32

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.833

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.723

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.767

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

GnomAD4 genome AF: 0.806 AC: 122691 AN: 152210 Hom.: 49793 Cov.: 32 AF XY: 0.811 AC XY: 60329 AN XY: 74406

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.723

Gnomad4 EAS AF: 0.823

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.829

Gnomad4 NFE AF: 0.751

Gnomad4 OTH AF: 0.767

Alfa AF: 0.765 Hom.: 22504

Bravo AF: 0.807

Asia WGS AF: 0.822 AC: 2858 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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

Other links and lift over

dbSNP: rs3783332; hg19: chr14-100586757;