rs242928

Variant names:

• chr17-45865685-G-A
• rs242928
• ENST00000579599.1:n.903-21524C>T

Variant summary

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

The ENST00000579599.1(MAPT-AS1):​n.903-21524C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,044 control chromosomes in the GnomAD database, including 15,138 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 0.44 (15138 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 16 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]

ENSG00000303280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 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.35-21524C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000579599.1	TSL:1	n.903-21524C>T		intron	N/A
	MAPT-AS1	ENST00000579244.1	TSL:2	n.122-21524C>T		intron	N/A
	MAPT-AS1	ENST00000634876.2	TSL:5	n.183-21524C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67278 AN: 151926 Hom.: 15123 Cov.: 32

Gnomad AFR AF: 0.432

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.438

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.443 AC: 67332 AN: 152044 Hom.: 15138 Cov.: 32 AF XY: 0.448 AC XY: 33327 AN XY: 74318

African (AFR) AF: 0.432 AC: 17921 AN: 41466

American (AMR) AF: 0.483 AC: 7393 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.268 AC: 1390 AN: 5182

South Asian (SAS) AF: 0.435 AC: 2099 AN: 4822

European-Finnish (FIN) AF: 0.550 AC: 5798 AN: 10544

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29759 AN: 67954

Other (OTH) AF: 0.437 AC: 923 AN: 2110

Alfa AF: 0.437 Hom.: 17329

Bravo AF: 0.434

Asia WGS AF: 0.381 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.55
PhyloP100		0.35

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: rs242928;

hg19: chr17-43943051;