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GeneBe

14-99937279-A-G

Variant summary

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

The NM_004434.3(EML1):c.2096-538A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 152,176 control chromosomes in the GnomAD database, including 45,880 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 0.77 ( 45880 hom., cov: 32)

Consequence

EML1
NM_004434.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.419
Variant links:
Genes affected
EML1 (HGNC:3330): (EMAP like 1) Human echinoderm microtubule-associated protein-like is a strong candidate for the Usher syndrome type 1A gene. Usher syndromes (USHs) are a group of genetic disorders consisting of congenital deafness, retinitis pigmentosa, and vestibular dysfunction of variable onset and severity depending on the genetic type. The disease process in USHs involves the entire brain and is not limited to the posterior fossa or auditory and visual systems. The USHs are catagorized as type I (USH1A, USH1B, USH1C, USH1D, USH1E and USH1F), type II (USH2A and USH2B) and type III (USH3). The type I is the most severe form. Gene loci responsible for these three types are all mapped. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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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=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EML1NM_004434.3 linkuse as main transcriptc.2096-538A>G intron_variant ENST00000262233.11

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EML1ENST00000262233.11 linkuse as main transcriptc.2096-538A>G intron_variant 1 NM_004434.3 P1O00423-1

Frequencies

GnomAD3 genomes
AF:
0.772
AC:
117461
AN:
152058
Hom.:
45840
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.891
Gnomad AMI
AF:
0.665
Gnomad AMR
AF:
0.708
Gnomad ASJ
AF:
0.724
Gnomad EAS
AF:
0.665
Gnomad SAS
AF:
0.638
Gnomad FIN
AF:
0.807
Gnomad MID
AF:
0.750
Gnomad NFE
AF:
0.732
Gnomad OTH
AF:
0.763
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.772
AC:
117549
AN:
152176
Hom.:
45880
Cov.:
32
AF XY:
0.772
AC XY:
57400
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.891
Gnomad4 AMR
AF:
0.707
Gnomad4 ASJ
AF:
0.724
Gnomad4 EAS
AF:
0.664
Gnomad4 SAS
AF:
0.637
Gnomad4 FIN
AF:
0.807
Gnomad4 NFE
AF:
0.732
Gnomad4 OTH
AF:
0.761
Alfa
AF:
0.733
Hom.:
65209
Bravo
AF:
0.769
Asia WGS
AF:
0.693
AC:
2412
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
Cadd
Benign
4.1
Dann
Benign
0.37

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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.

Other links and lift over

dbSNP: rs11160562; hg19: chr14-100403616; COSMIC: COSV51742908; API