rs7641464

Variant names:

• chr3-116167423-G-A
• rs7641464
• NM_002338.5:c.156-80867C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-116167423-G-A
• chr3-116167423-G-C
• chr3-116167423-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002338.5(LSAMP):​c.156-80867C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,020 control chromosomes in the GnomAD database, including 23,266 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 (23266 hom., cov: 33)
• Consequence: LSAMP NM_002338.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0990

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LSAMP	NM_002338.5	c.156-80867C>T		intron_variant	Intron 1 of 6	ENST00000490035.7	NP_002329.2
LSAMP	NM_001318915.2	c.156-80867C>T		intron_variant	Intron 1 of 8		NP_001305844.1
LSAMP	XM_017006383.3	c.156-80867C>T		intron_variant	Intron 1 of 7		XP_016861872.1
LSAMP	XM_011512840.4	c.156-80867C>T		intron_variant	Intron 1 of 7		XP_011511142.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LSAMP	ENST00000490035.7	c.156-80867C>T		intron_variant	Intron 1 of 6	1	NM_002338.5	ENSP00000419000.1
LSAMP	ENST00000333617.8	c.108-80867C>T		intron_variant	Intron 1 of 8	2		ENSP00000328455.4
LSAMP	ENST00000474851.1	c.258-80867C>T		intron_variant	Intron 3 of 4	5		ENSP00000418506.1

Frequencies

GnomAD3 genomes AF: 0.540 AC: 81993 AN: 151902 Hom.: 23269 Cov.: 33

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.678

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.589

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.539 AC: 82008 AN: 152020 Hom.: 23266 Cov.: 33 AF XY: 0.543 AC XY: 40346 AN XY: 74296

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.590

Alfa AF: 0.595 Hom.: 25486

Bravo AF: 0.525

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.47

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

Other links and lift over

dbSNP: rs7641464; hg19: chr3-115886270;