Variant 2-54854239-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001039753.4(EML6):c.1657+384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,028 control chromosomes in the GnomAD database, including 4,039 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 0.22 ( 4039 hom., cov: 33)

Consequence

EML6
NM_001039753.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.692

Variant links:

Genes affected

EML6 (HGNC:35412): (EMAP like 6) Predicted to enable microtubule binding activity. Predicted to be located in cytoplasm and microtubule. [provided by Alliance of Genome Resources, Apr 2022]

EML6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.42).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EML6	NM_001039753.4 linkuse as main transcript	c.1657+384C>T		intron_variant		ENST00000356458.8	NP_001034842.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
EML6	ENST00000356458.8 linkuse as main transcript	c.1657+384C>T	intron_variant	5	NM_001039753.4	ENSP00000348842	P1	Q6ZMW3-1
EML6	ENST00000673912.1 linkuse as main transcript	c.1657+384C>T	intron_variant, NMD_transcript_variant			ENSP00000501234
EML6	ENST00000493997.1 linkuse as main transcript	n.5+384C>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.220

AC:

33454

AN:

151912

Hom.:

4039

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.250

Gnomad EAS

AF:

0.0739

Gnomad SAS

AF:

0.125

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.288

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.245

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

GnomAD4 genome

AF:

0.220

AC:

33464

AN:

152028

Hom.:

4039

Cov.:

AF XY:

0.218

AC XY:

16184

AN XY:

74292

show subpopulations

Gnomad4 AFR

AF:

0.164

Gnomad4 AMR

AF:

0.215

Gnomad4 ASJ

AF:

0.250

Gnomad4 EAS

AF:

0.0741

Gnomad4 SAS

AF:

0.125

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.247

Alfa

AF:

0.256

Hom.:

10162

Bravo

AF:

0.214

Asia WGS

AF:

0.131

AC:

455

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Benign

0.85

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over