rs2019820

Variant names:

• chr17-45882459-C-T
• rs2019820
• ENST00000579599.1:n.902+12153G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579599.1(MAPT-AS1):​n.902+12153G>A variant causes a intron 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 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.392
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579599.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	NR_024559.1		n.34+13021G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000579599.1	TSL:1	n.902+12153G>A		intron	N/A
	MAPT-AS1	ENST00000579244.1	TSL:2	n.121+13021G>A		intron	N/A
	MAPT-AS1	ENST00000634876.2	TSL:5	n.182+13021G>A		intron	N/A

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

African (AFR) AF: 0.115 AC: 4758 AN: 41452

American (AMR) AF: 0.0682 AC: 1041 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3472

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5150

South Asian (SAS) AF: 0.0564 AC: 271 AN: 4806

European-Finnish (FIN) AF: 0.143 AC: 1506 AN: 10552

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7960 AN: 67932

Other (OTH) AF: 0.0881 AC: 186 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	3.6
DANN	Benign	0.84
PhyloP100		0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2019820;

hg19: chr17-43959825;