rs10132509

chr14-88737437-A-G

Variant summary

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

The NM_183387.3(EML5):c.848-872T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,134 control chromosomes in the GnomAD database, including 35,896 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 0.67 (35896 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EML5	NM_183387.3	c.848-872T>C		intron_variant		ENST00000554922.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EML5	ENST00000554922.6	c.848-872T>C		intron_variant		5	NM_183387.3	P4
EML5	ENST00000380664.9	c.848-872T>C		intron_variant		5		A1

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101067 AN: 152016 Hom.: 35815 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.943

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.613

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

GnomAD4 genome AF: 0.665 AC: 101210 AN: 152134 Hom.: 35896 Cov.: 32 AF XY: 0.665 AC XY: 49457 AN XY: 74372

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.944

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.618

Alfa AF: 0.593 Hom.: 6753

Bravo AF: 0.690

Asia WGS AF: 0.852 AC: 2964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.2
Dann	Benign	0.60

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: rs10132509; hg19: chr14-89203781;