14-88668016-C-T

Variant names:

• chr14-88668016-C-T
• rs1956411
• NM_183387.3:c.3125-2527G>A

Variant summary

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

The NM_183387.3(EML5):​c.3125-2527G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,052 control chromosomes in the GnomAD database, including 34,092 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 0.65 (34092 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

EML5 (HGNC:18197): (EMAP like 5) Predicted to enable microtubule binding activity. Located in extracellular exosome. [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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EML5	NM_183387.3	c.3125-2527G>A		intron_variant	Intron 21 of 43	ENST00000554922.6	NP_899243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EML5	ENST00000554922.6	c.3125-2527G>A		intron_variant	Intron 21 of 43	5	NM_183387.3	ENSP00000451998.1
EML5	ENST00000380664.9	c.3125-2527G>A		intron_variant	Intron 21 of 41	5		ENSP00000370039.5
EML5	ENST00000553281.5	n.*1296-2527G>A		intron_variant	Intron 14 of 28	2		ENSP00000452360.1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98768 AN: 151934 Hom.: 34024 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.650 AC: 98890 AN: 152052 Hom.: 34092 Cov.: 32 AF XY: 0.648 AC XY: 48158 AN XY: 74288

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.666

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.594

Alfa AF: 0.604 Hom.: 5020

Bravo AF: 0.677

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.79
DANN	Benign	0.32

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: rs1956411; hg19: chr14-89134360;