Variant rs1961245 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001039753.4(EML6):c.1933-61G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 845,580 control chromosomes in the GnomAD database, including 73,407 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 0.45 ( 16240 hom., cov: 32)

Exomes 𝑓: 0.40 ( 57167 hom. )

Consequence

EML6
NM_001039753.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.00

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EML6	NM_001039753.4 linkuse as main transcript	c.1933-61G>A		intron_variant		ENST00000356458.8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris	UniProt
EML6	ENST00000356458.8 linkuse as main transcript	c.1933-61G>A	intron_variant	5	NM_001039753.4	P1	Q6ZMW3-1
EML6	ENST00000673912.1 linkuse as main transcript	c.1933-61G>A	intron_variant, NMD_transcript_variant
EML6	ENST00000493997.1 linkuse as main transcript	n.281-61G>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.448

AC:

68112

AN:

151922

Hom.:

16222

Cov.:

show subpopulations

Gnomad AFR

AF:

0.597

Gnomad AMI

AF:

0.467

Gnomad AMR

AF:

0.414

Gnomad ASJ

AF:

0.405

Gnomad EAS

AF:

0.547

Gnomad SAS

AF:

0.565

Gnomad FIN

AF:

0.443

Gnomad MID

AF:

0.323

Gnomad NFE

AF:

0.353

Gnomad OTH

AF:

0.440

GnomAD4 exome

AF:

0.396

AC:

274347

AN:

693540

Hom.:

57167

AF XY:

0.402

AC XY:

144208

AN XY:

358838

show subpopulations

Gnomad4 AFR exome

AF:

0.614

Gnomad4 AMR exome

AF:

0.413

Gnomad4 ASJ exome

AF:

0.398

Gnomad4 EAS exome

AF:

0.549

Gnomad4 SAS exome

AF:

0.559

Gnomad4 FIN exome

AF:

0.423

Gnomad4 NFE exome

AF:

0.355

Gnomad4 OTH exome

AF:

0.411

GnomAD4 genome

AF:

0.448

AC:

68181

AN:

152040

Hom.:

16240

Cov.:

AF XY:

0.453

AC XY:

33705

AN XY:

74330

show subpopulations

Gnomad4 AFR

AF:

0.597

Gnomad4 AMR

AF:

0.414

Gnomad4 ASJ

AF:

0.405

Gnomad4 EAS

AF:

0.546

Gnomad4 SAS

AF:

0.566

Gnomad4 FIN

AF:

0.443

Gnomad4 NFE

AF:

0.354

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.390

Hom.:

6589

Bravo

AF:

0.451

Asia WGS

AF:

0.554

AC:

1925

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.16

DANN

Benign

0.19

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