rs2019820

Positions:

• chr17-45882459-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392

Genes affected

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

ACMG classification

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	UniProt
MAPT-AS1	NR_024559.1	n.34+13021G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPT-AS1	ENST00000634876.2	n.182+13021G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16432 AN: 151816 Hom.: 928 Cov.: 31

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

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

Other links and lift over

dbSNP: rs2019820; hg19: chr17-43959825;