17-45858265-T-C

Variant names:

• chr17-45858265-T-C
• rs962885
• ENST00000579599.1:n.903-14104A>G

Variant summary

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

The ENST00000579599.1(MAPT-AS1):​n.903-14104A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 151,804 control chromosomes in the GnomAD database, including 26,263 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 0.58 (26263 hom., cov: 30)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.196
• Publications: 12 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.652 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.35-14104A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000579599.1	TSL:1	n.903-14104A>G		intron	N/A
	MAPT-AS1	ENST00000579244.1	TSL:2	n.122-14104A>G		intron	N/A
	MAPT-AS1	ENST00000634876.2	TSL:5	n.183-14104A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87562 AN: 151686 Hom.: 26253 Cov.: 30

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.774

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.577 AC: 87599 AN: 151804 Hom.: 26263 Cov.: 30 AF XY: 0.574 AC XY: 42595 AN XY: 74146

African (AFR) AF: 0.431 AC: 17829 AN: 41352

American (AMR) AF: 0.659 AC: 10047 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1478 AN: 5136

South Asian (SAS) AF: 0.515 AC: 2466 AN: 4790

European-Finnish (FIN) AF: 0.632 AC: 6668 AN: 10548

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44629 AN: 67942

Other (OTH) AF: 0.606 AC: 1275 AN: 2104

Alfa AF: 0.630 Hom.: 60428

Bravo AF: 0.570

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		-0.20

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: rs962885;

hg19: chr17-43935631;