chr17-45861104-A-G

Variant names:

• chr17-45861104-A-G
• rs242933
• ENST00000579599.1:n.903-16943T>C

Variant summary

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

The ENST00000579599.1(MAPT-AS1):​n.903-16943T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 152,052 control chromosomes in the GnomAD database, including 34,793 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 0.67 (34793 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.712 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.35-16943T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000579599.1	TSL:1	n.903-16943T>C		intron	N/A
	MAPT-AS1	ENST00000579244.1	TSL:2	n.122-16943T>C		intron	N/A
	MAPT-AS1	ENST00000634876.2	TSL:5	n.183-16943T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.675 AC: 102481 AN: 151934 Hom.: 34760 Cov.: 32

Gnomad AFR AF: 0.650

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.675 AC: 102564 AN: 152052 Hom.: 34793 Cov.: 32 AF XY: 0.671 AC XY: 49898 AN XY: 74316

African (AFR) AF: 0.650 AC: 26962 AN: 41450

American (AMR) AF: 0.723 AC: 11057 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2522 AN: 3470

East Asian (EAS) AF: 0.435 AC: 2244 AN: 5162

South Asian (SAS) AF: 0.610 AC: 2938 AN: 4816

European-Finnish (FIN) AF: 0.660 AC: 6981 AN: 10582

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47482 AN: 67968

Other (OTH) AF: 0.682 AC: 1441 AN: 2114

Alfa AF: 0.691 Hom.: 53809

Bravo AF: 0.676

Asia WGS AF: 0.557 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.52
PhyloP100		-0.11

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: rs242933;

hg19: chr17-43938470;