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11-131911625-G-T

Variant summary

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

The NM_001352005.2(NTM):c.144G>T(p.Arg48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00211 in 1,614,176 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0023 ( 5 hom., cov: 33)
Exomes 𝑓: 0.0021 ( 69 hom. )

Consequence

NTM
NM_001352005.2 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.33
Variant links:
Genes affected
NTM (HGNC:17941): (neurotrimin) This gene encodes a member of the IgLON (LAMP, OBCAM, Ntm) family of immunoglobulin (Ig) domain-containing glycosylphosphatidylinositol (GPI)-anchored cell adhesion molecules. The encoded protein may promote neurite outgrowth and adhesion via a homophilic mechanism. This gene is closely linked to a related family member, opioid binding protein/cell adhesion molecule-like (OPCML), on chromosome 11. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2009]

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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=-0.48).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-131911625-G-T is Benign according to our data. Variant chr11-131911625-G-T is described in ClinVar as [Benign]. Clinvar id is 721283.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=3.34 with no splicing effect.
BS1
?
    BS1 - Allele frequency is greater than expected for disorder
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00235 (358/152350) while in subpopulation EAS AF= 0.0492 (254/5160). AF 95% confidence interval is 0.0443. There are 5 homozygotes in gnomad4. There are 177 alleles in male gnomad4 subpopulation. Median coverage is 33. 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 5 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NTMNM_001352005.2 linkuse as main transcriptc.144G>T p.Arg48= synonymous_variant 2/9 ENST00000683400.1
LOC107984413XR_007062957.1 linkuse as main transcript upstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NTMENST00000683400.1 linkuse as main transcriptc.144G>T p.Arg48= synonymous_variant 2/9 NM_001352005.2 A1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00235
AC:
358
AN:
152232
Hom.:
5
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000362
Gnomad AMI
AF:
0.00219
Gnomad AMR
AF:
0.000589
Gnomad ASJ
AF:
0.000288
Gnomad EAS
AF:
0.0491
Gnomad SAS
AF:
0.00311
Gnomad FIN
AF:
0.0000941
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.000808
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.00437
AC:
1099
AN:
251328
Hom.:
18
AF XY:
0.00402
AC XY:
546
AN XY:
135844
show subpopulations
Gnomad AFR exome
AF:
0.000308
Gnomad AMR exome
AF:
0.000463
Gnomad ASJ exome
AF:
0.0000992
Gnomad EAS exome
AF:
0.0487
Gnomad SAS exome
AF:
0.00216
Gnomad FIN exome
AF:
0.000231
Gnomad NFE exome
AF:
0.000827
Gnomad OTH exome
AF:
0.00261
GnomAD4 exome
AF:
0.00209
AC:
3051
AN:
1461826
Hom.:
69
Cov.:
32
AF XY:
0.00207
AC XY:
1506
AN XY:
727220
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.000425
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.0499
Gnomad4 SAS exome
AF:
0.00245
Gnomad4 FIN exome
AF:
0.000300
Gnomad4 NFE exome
AF:
0.000468
Gnomad4 OTH exome
AF:
0.00475
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00235
AC:
358
AN:
152350
Hom.:
5
Cov.:
33
AF XY:
0.00238
AC XY:
177
AN XY:
74490
show subpopulations
Gnomad4 AFR
AF:
0.000361
Gnomad4 AMR
AF:
0.000588
Gnomad4 ASJ
AF:
0.000288
Gnomad4 EAS
AF:
0.0492
Gnomad4 SAS
AF:
0.00311
Gnomad4 FIN
AF:
0.0000941
Gnomad4 NFE
AF:
0.000808
Gnomad4 OTH
AF:
0.00237
Alfa
AF:
0.000914
Hom.:
0
Bravo
AF:
0.00249
EpiCase
AF:
0.000273
EpiControl
AF:
0.000237

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 testingInvitaeApr 10, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.48
Cadd
Benign
16
Dann
Benign
0.93

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: rs75710163; hg19: chr11-131781519; COSMIC: COSV66180593; COSMIC: COSV66180593; API