GeneBe

chr10-103479506-T-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000453753.5(NEURL1-AS1):​n.*97A>T variant causes a downstream gene 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: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

NEURL1-AS1
ENST00000453753.5 downstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.570

Publications

7 publications found
Variant links:
Genes affected
NEURL1-AS1 (HGNC:51220): (NEURL1 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NEURL1-AS1NR_120675.1 linkn.*97A>T downstream_gene_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NEURL1-AS1ENST00000453753.5 linkn.*97A>T downstream_gene_variant 5
NEURL1-AS1ENST00000783100.1 linkn.*97A>T downstream_gene_variant

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
5164
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
2674
African (AFR)
AF:
0.00
AC:
0
AN:
198
American (AMR)
AF:
0.00
AC:
0
AN:
1156
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
114
East Asian (EAS)
AF:
0.00
AC:
0
AN:
198
South Asian (SAS)
AF:
0.00
AC:
0
AN:
326
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
72
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
10
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
2830
Other (OTH)
AF:
0.00
AC:
0
AN:
260
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
1.7
DANN
Benign
0.71
PhyloP100
-0.57
PromoterAI
0.0096
Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs1555823; hg19: chr10-105239263; API