dbSNP rs2289271: LSAMP:c.*404G>A (chr3-115809913-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002338.5(LSAMP):c.*404G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 157,816 control chromosomes in the GnomAD database, including 24,127 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 0.54 ( 23688 hom., cov: 31)

Exomes 𝑓: 0.36 ( 439 hom. )

Consequence

LSAMP
NM_002338.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.36

Publications

7 publications found

Variant links:

Genes affected

LSAMP (HGNC:6705): (limbic system associated membrane protein) This gene encodes a member of the immunoglobulin LAMP, OBCAM and neurotrimin (IgLON) family of proteins. The encoded preproprotein is proteolytically processed to generate a neuronal surface glycoprotein. This protein may act as a selective homophilic adhesion molecule during axon guidance and neuronal growth in the developing limbic system. The encoded protein may also function as a tumor suppressor and may play a role in neuropsychiatric disorders. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

LSAMP links:

ENSG00000297708 (HGNC:):

ENSG00000297708 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.59).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSAMP	NM_002338.5 link	c.*404G>A		3_prime_UTR_variant	Exon 7 of 7	ENST00000490035.7	NP_002329.2	Q13449B7Z661

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
LSAMP	ENST00000490035.7 link	c.*404G>A	3_prime_UTR_variant	Exon 7 of 7	1	NM_002338.5	ENSP00000419000.1	Q13449
LSAMP	ENST00000333617.8 link	c.*404G>A	3_prime_UTR_variant	Exon 9 of 9	2		ENSP00000328455.4	H3BLU2
ENSG00000297708	ENST00000750388.1 link	n.171-499C>T	intron_variant	Intron 1 of 2
ENSG00000297708	ENST00000750389.1 link	n.145-499C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.536

AC:

81257

AN:

151666

Hom.:

23651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.790

Gnomad AMI

AF:

0.393

Gnomad AMR

AF:

0.514

Gnomad ASJ

AF:

0.419

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.408

Gnomad FIN

AF:

0.470

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.426

Gnomad OTH

AF:

0.547

GnomAD4 exome

AF:

0.360

AC:

2170

AN:

6032

Hom.:

439

Cov.:

AF XY:

0.363

AC XY:

1165

AN XY:

3212

show subpopulations

African (AFR)

AF:

0.759

AC:

AN:

116

American (AMR)

AF:

0.399

AC:

AN:

158

Ashkenazi Jewish (ASJ)

AF:

0.331

AC:

AN:

166

East Asian (EAS)

AF:

0.200

AC:

AN:

170

South Asian (SAS)

AF:

0.265

AC:

AN:

302

European-Finnish (FIN)

AF:

0.347

AC:

AN:

248

Middle Eastern (MID)

AF:

0.192

AC:

AN:

European-Non Finnish (NFE)

AF:

0.363

AC:

1628

AN:

4484

Other (OTH)

AF:

0.362

AC:

131

AN:

362

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

134

202

269

336

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.536

AC:

81334

AN:

151784

Hom.:

23688

Cov.:

AF XY:

0.536

AC XY:

39748

AN XY:

74178

show subpopulations

African (AFR)

AF:

0.790

AC:

32709

AN:

41382

American (AMR)

AF:

0.513

AC:

7833

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.419

AC:

1453

AN:

3464

East Asian (EAS)

AF:

0.358

AC:

1837

AN:

5136

South Asian (SAS)

AF:

0.407

AC:

1954

AN:

4804

European-Finnish (FIN)

AF:

0.470

AC:

4953

AN:

10532

Middle Eastern (MID)

AF:

0.572

AC:

167

AN:

292

European-Non Finnish (NFE)

AF:

0.426

AC:

28926

AN:

67900

Other (OTH)

AF:

0.543

AC:

1144

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1692

3383

5075

6766

8458

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.457

Hom.:

29140

Bravo

AF:

0.550

Asia WGS

AF:

0.398

AC:

1387

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

(source)

DANN

Benign

0.83

PhyloP100

3.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over