17-45882459-C-T

Variant summary

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

The NR_024559.1(MAPT-AS1):​n.34+13021G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 151,934 control chromosomes in the GnomAD database, including 929 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 0.11 ( 929 hom., cov: 31)

Consequence

MAPT-AS1
NR_024559.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.392
Variant links:
Genes affected
MAPT-AS1 (HGNC:43738): (MAPT antisense RNA 1) Implicated in Parkinson's disease. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.115 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
MAPT-AS1NR_024559.1 linkuse as main transcriptn.34+13021G>A intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
MAPT-AS1ENST00000634876.2 linkuse as main transcriptn.182+13021G>A intron_variant, non_coding_transcript_variant 5

Frequencies

GnomAD3 genomes
AF:
0.108
AC:
16432
AN:
151816
Hom.:
928
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.115
Gnomad AMI
AF:
0.0769
Gnomad AMR
AF:
0.0685
Gnomad ASJ
AF:
0.148
Gnomad EAS
AF:
0.0153
Gnomad SAS
AF:
0.0568
Gnomad FIN
AF:
0.143
Gnomad MID
AF:
0.133
Gnomad NFE
AF:
0.117
Gnomad OTH
AF:
0.0890
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.108
AC:
16426
AN:
151934
Hom.:
929
Cov.:
31
AF XY:
0.109
AC XY:
8067
AN XY:
74268
show subpopulations
Gnomad4 AFR
AF:
0.115
Gnomad4 AMR
AF:
0.0682
Gnomad4 ASJ
AF:
0.148
Gnomad4 EAS
AF:
0.0153
Gnomad4 SAS
AF:
0.0564
Gnomad4 FIN
AF:
0.143
Gnomad4 NFE
AF:
0.117
Gnomad4 OTH
AF:
0.0881
Alfa
AF:
0.114
Hom.:
110
Bravo
AF:
0.103
Asia WGS
AF:
0.0410
AC:
144
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
3.6
DANN
Benign
0.84

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: rs2019820; hg19: chr17-43959825; API