rs941900

chr14-100137062-C-Achr14-100137062-C-G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.907

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.896 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EVL	NM_016337.3	c.965-516C>A		intron_variant		ENST00000392920.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EVL	ENST00000392920.8	c.965-516C>A		intron_variant		1	NM_016337.3	P1

Frequencies

GnomAD3 genomes AF: 0.803 AC: 122064 AN: 152052 Hom.: 49353 Cov.: 33

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.: 0 AF XY: 0.672 AC XY: 2450 AN XY: 3648

Gnomad4 AFR exome AF: 0.764

Gnomad4 AMR exome AF: 0.749

Gnomad4 ASJ exome AF: 0.613

Gnomad4 EAS exome AF: 0.680

Gnomad4 SAS exome AF: 0.625

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.647

Gnomad4 OTH exome AF: 0.677

GnomAD4 genome AF: 0.803 AC: 122174 AN: 152170 Hom.: 49404 Cov.: 33 AF XY: 0.807 AC XY: 60003 AN XY: 74398

Gnomad4 AFR AF: 0.903

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.820

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.749

Gnomad4 OTH AF: 0.766

Alfa AF: 0.745 Hom.: 49649

Bravo AF: 0.805

Asia WGS AF: 0.818 AC: 2843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.44

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

Other links and lift over

dbSNP: rs941900; hg19: chr14-100603399;