ENST00000634876.2:n.604-6817C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000634876.2(MAPT-AS1):​n.604-6817C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,002 control chromosomes in the GnomAD database, including 24,302 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 0.56 ( 24302 hom., cov: 32)

Consequence

MAPT-AS1
ENST00000634876.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.210

Publications

11 publications found
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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MAPT-AS1ENST00000634876.2 linkn.604-6817C>A intron_variant Intron 2 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.557
AC:
84534
AN:
151884
Hom.:
24298
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.436
Gnomad AMI
AF:
0.594
Gnomad AMR
AF:
0.611
Gnomad ASJ
AF:
0.541
Gnomad EAS
AF:
0.808
Gnomad SAS
AF:
0.767
Gnomad FIN
AF:
0.707
Gnomad MID
AF:
0.560
Gnomad NFE
AF:
0.561
Gnomad OTH
AF:
0.538
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.556
AC:
84558
AN:
152002
Hom.:
24302
Cov.:
32
AF XY:
0.569
AC XY:
42290
AN XY:
74300
show subpopulations
African (AFR)
AF:
0.435
AC:
18036
AN:
41422
American (AMR)
AF:
0.612
AC:
9350
AN:
15284
Ashkenazi Jewish (ASJ)
AF:
0.541
AC:
1876
AN:
3468
East Asian (EAS)
AF:
0.807
AC:
4162
AN:
5156
South Asian (SAS)
AF:
0.768
AC:
3705
AN:
4822
European-Finnish (FIN)
AF:
0.707
AC:
7485
AN:
10580
Middle Eastern (MID)
AF:
0.537
AC:
158
AN:
294
European-Non Finnish (NFE)
AF:
0.561
AC:
38107
AN:
67958
Other (OTH)
AF:
0.540
AC:
1137
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1885
3770
5655
7540
9425
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
730
1460
2190
2920
3650
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.431
Hom.:
1198
Bravo
AF:
0.542
Asia WGS
AF:
0.753
AC:
2618
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
3.0
DANN
Benign
0.75
PhyloP100
-0.21

Splicing

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

Publications

Other links and lift over

dbSNP: rs242948; hg19: chr17-43913544; API