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GeneBe

X-37659631-G-A

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001170331.2(LANCL3):c.867G>A(p.Glu289=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00198 in 1,208,178 control chromosomes in the GnomAD database, including 21 homozygotes. There are 647 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.010 ( 14 hom., 284 hem., cov: 22)
Exomes 𝑓: 0.0012 ( 7 hom. 363 hem. )

Consequence

LANCL3
NM_001170331.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.13
Variant links:
Genes affected
LANCL3 (HGNC:24767): (LanC like family member 3) Predicted to be involved in carbohydrate metabolic process. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.47).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant X-37659631-G-A is Benign according to our data. Variant chrX-37659631-G-A is described in ClinVar as [Benign]. Clinvar id is 781640.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=2.13 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.01 (1111/110587) while in subpopulation AFR AF= 0.0342 (1037/30306). AF 95% confidence interval is 0.0325. There are 14 homozygotes in gnomad4. There are 284 alleles in male gnomad4 subpopulation. Median coverage is 22. This position pass quality control queck.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 14 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LANCL3NM_001170331.2 linkuse as main transcriptc.867G>A p.Glu289= synonymous_variant 3/5 ENST00000378619.4
LANCL3NM_198511.3 linkuse as main transcriptc.867G>A p.Glu289= synonymous_variant 3/6
LANCL3XM_011543904.3 linkuse as main transcriptc.321G>A p.Glu107= synonymous_variant 3/5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LANCL3ENST00000378619.4 linkuse as main transcriptc.867G>A p.Glu289= synonymous_variant 3/51 NM_001170331.2 P1Q6ZV70-1
LANCL3ENST00000378621.7 linkuse as main transcriptc.867G>A p.Glu289= synonymous_variant 3/61 Q6ZV70-2
LANCL3ENST00000614025.4 linkuse as main transcriptc.867G>A p.Glu289= synonymous_variant 3/52 Q6ZV70-2

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00998
AC:
1103
AN:
110534
Hom.:
14
Cov.:
22
AF XY:
0.00858
AC XY:
281
AN XY:
32752
show subpopulations
Gnomad AFR
AF:
0.0340
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00481
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00837
Gnomad NFE
AF:
0.000151
Gnomad OTH
AF:
0.00945
GnomAD3 exomes
AF:
0.00312
AC:
569
AN:
182533
Hom.:
7
AF XY:
0.00211
AC XY:
142
AN XY:
67205
show subpopulations
Gnomad AFR exome
AF:
0.0379
Gnomad AMR exome
AF:
0.00208
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000105
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000369
Gnomad OTH exome
AF:
0.00200
GnomAD4 exome
AF:
0.00116
AC:
1277
AN:
1097591
Hom.:
7
Cov.:
31
AF XY:
0.00100
AC XY:
363
AN XY:
363017
show subpopulations
Gnomad4 AFR exome
AF:
0.0367
Gnomad4 AMR exome
AF:
0.00253
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000203
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000725
Gnomad4 OTH exome
AF:
0.00278
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0100
AC:
1111
AN:
110587
Hom.:
14
Cov.:
22
AF XY:
0.00865
AC XY:
284
AN XY:
32815
show subpopulations
Gnomad4 AFR
AF:
0.0342
Gnomad4 AMR
AF:
0.00480
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000151
Gnomad4 OTH
AF:
0.00933
Alfa
AF:
0.00416
Hom.:
32
Bravo
AF:
0.0121
EpiCase
AF:
0.000109
EpiControl
AF:
0.000178

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 12, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.47
Cadd
Benign
5.6
Dann
Benign
0.82
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs142780377; hg19: chrX-37518884; API