rs2395402

Variant summary

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

The NM_181336.4(LEMD2):​c.777+838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,148 control chromosomes in the GnomAD database, including 18,970 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 0.48 ( 18970 hom., cov: 33)

Consequence

LEMD2
NM_181336.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.104
Variant links:
Genes affected
LEMD2 (HGNC:21244): (LEM domain nuclear envelope protein 2) This gene encodes a LEM domain-containing transmembrane protein of the inner nuclear membrane. The protein is involved in nuclear structure organization and plays a role in cell signaling and differentiation. Mutations in this gene result in Cataract 46, juvenile-onset. Multiple transcript variants have been found for this gene. [provided by RefSeq, Feb 2017]

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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=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LEMD2NM_181336.4 linkuse as main transcriptc.777+838C>T intron_variant ENST00000293760.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LEMD2ENST00000293760.10 linkuse as main transcriptc.777+838C>T intron_variant 1 NM_181336.4 P1Q8NC56-1

Frequencies

GnomAD3 genomes
AF:
0.481
AC:
73105
AN:
152030
Hom.:
18965
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.286
Gnomad AMI
AF:
0.566
Gnomad AMR
AF:
0.480
Gnomad ASJ
AF:
0.546
Gnomad EAS
AF:
0.817
Gnomad SAS
AF:
0.664
Gnomad FIN
AF:
0.538
Gnomad MID
AF:
0.620
Gnomad NFE
AF:
0.546
Gnomad OTH
AF:
0.506
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.481
AC:
73129
AN:
152148
Hom.:
18970
Cov.:
33
AF XY:
0.482
AC XY:
35819
AN XY:
74390
show subpopulations
Gnomad4 AFR
AF:
0.286
Gnomad4 AMR
AF:
0.480
Gnomad4 ASJ
AF:
0.546
Gnomad4 EAS
AF:
0.817
Gnomad4 SAS
AF:
0.665
Gnomad4 FIN
AF:
0.538
Gnomad4 NFE
AF:
0.546
Gnomad4 OTH
AF:
0.510
Alfa
AF:
0.543
Hom.:
43003
Bravo
AF:
0.469
Asia WGS
AF:
0.677
AC:
2355
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
4.6
DANN
Benign
0.50

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.

Other links and lift over

dbSNP: rs2395402; hg19: chr6-33753673; API