14-88643951-A-G

Position:

• chr14-88643951-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.4107+482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.839 in 152,160 control chromosomes in the GnomAD database, including 54,056 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 0.84 (54056 hom., cov: 32)
• Consequence: EML5 NM_183387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.528

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]

EML5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EML5	NM_183387.3	c.4107+482T>C		intron_variant		ENST00000554922.6	NP_899243.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EML5	ENST00000554922.6	c.4107+482T>C		intron_variant		5	NM_183387.3	ENSP00000451998.1

Frequencies

GnomAD3 genomes AF: 0.839 AC: 127535 AN: 152044 Hom.: 54006 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.905

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.766

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.839 AC: 127638 AN: 152160 Hom.: 54056 Cov.: 32 AF XY: 0.841 AC XY: 62577 AN XY: 74390

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.905

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.880

Gnomad4 OTH AF: 0.873

Alfa AF: 0.872 Hom.: 9138

Bravo AF: 0.838

Asia WGS AF: 0.850 AC: 2959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	11
DANN	Benign	0.21

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.20		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.20		Position offset: 44

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1144921; hg19: chr14-89110295;