chr15-74850420-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005697.5(SCAMP2):​c.632+94A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 1,117,448 control chromosomes in the GnomAD database, including 10,129 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 0.12 ( 1271 hom., cov: 32)
Exomes 𝑓: 0.13 ( 8858 hom. )

Consequence

SCAMP2
NM_005697.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.345
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SCAMP2NM_005697.5 linkuse as main transcriptc.632+94A>C intron_variant ENST00000268099.13
SCAMP2NM_001320778.2 linkuse as main transcriptc.761+94A>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SCAMP2ENST00000268099.13 linkuse as main transcriptc.632+94A>C intron_variant 1 NM_005697.5 P1

Frequencies

GnomAD3 genomes
AF:
0.119
AC:
18110
AN:
151752
Hom.:
1272
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0624
Gnomad AMI
AF:
0.0549
Gnomad AMR
AF:
0.149
Gnomad ASJ
AF:
0.141
Gnomad EAS
AF:
0.250
Gnomad SAS
AF:
0.143
Gnomad FIN
AF:
0.194
Gnomad MID
AF:
0.113
Gnomad NFE
AF:
0.124
Gnomad OTH
AF:
0.120
GnomAD4 exome
AF:
0.128
AC:
123904
AN:
965572
Hom.:
8858
AF XY:
0.129
AC XY:
63693
AN XY:
494986
show subpopulations
Gnomad4 AFR exome
AF:
0.0580
Gnomad4 AMR exome
AF:
0.169
Gnomad4 ASJ exome
AF:
0.135
Gnomad4 EAS exome
AF:
0.263
Gnomad4 SAS exome
AF:
0.145
Gnomad4 FIN exome
AF:
0.186
Gnomad4 NFE exome
AF:
0.116
Gnomad4 OTH exome
AF:
0.122
GnomAD4 genome
AF:
0.119
AC:
18103
AN:
151876
Hom.:
1271
Cov.:
32
AF XY:
0.124
AC XY:
9191
AN XY:
74210
show subpopulations
Gnomad4 AFR
AF:
0.0622
Gnomad4 AMR
AF:
0.149
Gnomad4 ASJ
AF:
0.141
Gnomad4 EAS
AF:
0.250
Gnomad4 SAS
AF:
0.142
Gnomad4 FIN
AF:
0.194
Gnomad4 NFE
AF:
0.124
Gnomad4 OTH
AF:
0.120
Alfa
AF:
0.123
Hom.:
1696
Bravo
AF:
0.112
Asia WGS
AF:
0.156
AC:
544
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
1.4
DANN
Benign
0.75
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2305668; hg19: chr15-75142761; COSMIC: COSV51513485; COSMIC: COSV51513485; API