rs12487

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_005697.5(SCAMP2):​c.*730A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)

Consequence

SCAMP2
NM_005697.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.21
Variant links:
Genes affected
SCAMP2 (HGNC:10564): (secretory carrier membrane protein 2) This gene product belongs to the SCAMP family of proteins which are secretory carrier membrane proteins. They function as carriers to the cell surface in post-golgi recycling pathways. Different family members are highly related products of distinct genes, and are usually expressed together. These findings suggest that the SCAMPs may function at the same site during vesicular transport rather than in separate pathways. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SCAMP2NM_005697.5 linkc.*730A>T 3_prime_UTR_variant 9/9 ENST00000268099.13 NP_005688.2 O15127A0A140VK92
SCAMP2NM_001320778.2 linkc.*730A>T 3_prime_UTR_variant 10/10 NP_001307707.1 A8K769

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SCAMP2ENST00000268099 linkc.*730A>T 3_prime_UTR_variant 9/91 NM_005697.5 ENSP00000268099.9 O15127
SCAMP2ENST00000566480 linkc.*1018A>T 3_prime_UTR_variant 7/75 ENSP00000455377.1 H3BPL9
SCAMP2ENST00000563663.5 linkn.*924A>T non_coding_transcript_exon_variant 4/45 ENSP00000455963.1 H3BQW2
SCAMP2ENST00000563663.5 linkn.*924A>T 3_prime_UTR_variant 4/45 ENSP00000455963.1 H3BQW2

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.41
DANN
Benign
0.70
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
2.1

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-75136694; API