14-88752194-C-G

Variant names:

• chr14-88752194-C-G
• rs10140896
• NM_183387.3:c.357+2318G>C

Variant summary

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

The NM_183387.3(EML5):​c.357+2318G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.637 in 151,984 control chromosomes in the GnomAD database, including 32,719 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 0.64 (32719 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.449
• Publications: 9 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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.357+2318G>C		intron_variant	Intron 2 of 43	ENST00000554922.6	NP_899243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EML5	ENST00000554922.6	c.357+2318G>C		intron_variant	Intron 2 of 43	5	NM_183387.3	ENSP00000451998.1
EML5	ENST00000380664.9	c.357+2318G>C		intron_variant	Intron 2 of 41	5		ENSP00000370039.5

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96632 AN: 151866 Hom.: 32651 Cov.: 32

Gnomad AFR AF: 0.844

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.589

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

GnomAD4 genome AF: 0.637 AC: 96755 AN: 151984 Hom.: 32719 Cov.: 32 AF XY: 0.635 AC XY: 47198 AN XY: 74280

African (AFR) AF: 0.844 AC: 35044 AN: 41498

American (AMR) AF: 0.658 AC: 10039 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1860 AN: 3470

East Asian (EAS) AF: 0.937 AC: 4842 AN: 5170

South Asian (SAS) AF: 0.674 AC: 3252 AN: 4822

European-Finnish (FIN) AF: 0.465 AC: 4904 AN: 10536

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34810 AN: 67924

Other (OTH) AF: 0.586 AC: 1235 AN: 2108

Alfa AF: 0.389 Hom.: 906

Bravo AF: 0.666

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.4
DANN	Benign	0.65
PhyloP100		-0.45
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: rs10140896; hg19: chr14-89218538;