20-18820026-C-T

Variant summary

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

The ENST00000623418.1(SCP2D1-AS1):​n.218+5240G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,160 control chromosomes in the GnomAD database, including 1,309 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 ( 1309 hom., cov: 32)

Consequence

SCP2D1-AS1
ENST00000623418.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.193
Variant links:
Genes affected
SCP2D1-AS1 (HGNC:16210): (SCP2D1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.68).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCP2D1-AS1NR_161342.1 linkn.268+5240G>A intron_variant Intron 2 of 2
SCP2D1-AS1NR_161343.1 linkn.244+5240G>A intron_variant Intron 2 of 2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCP2D1-AS1ENST00000623418.1 linkn.218+5240G>A intron_variant Intron 2 of 2 2

Frequencies

GnomAD3 genomes
AF:
0.117
AC:
17781
AN:
152042
Hom.:
1308
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0318
Gnomad AMI
AF:
0.141
Gnomad AMR
AF:
0.123
Gnomad ASJ
AF:
0.135
Gnomad EAS
AF:
0.0519
Gnomad SAS
AF:
0.105
Gnomad FIN
AF:
0.147
Gnomad MID
AF:
0.120
Gnomad NFE
AF:
0.167
Gnomad OTH
AF:
0.117
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.117
AC:
17782
AN:
152160
Hom.:
1309
Cov.:
32
AF XY:
0.115
AC XY:
8541
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0317
Gnomad4 AMR
AF:
0.123
Gnomad4 ASJ
AF:
0.135
Gnomad4 EAS
AF:
0.0515
Gnomad4 SAS
AF:
0.106
Gnomad4 FIN
AF:
0.147
Gnomad4 NFE
AF:
0.167
Gnomad4 OTH
AF:
0.115
Alfa
AF:
0.0949
Hom.:
199
Bravo
AF:
0.111
Asia WGS
AF:
0.0780
AC:
270
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.68
CADD
Benign
6.3
DANN
Benign
0.93

Splicing

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: rs41526044; hg19: chr20-18800670; API