chr17-45839770-G-A

Variant names:

• chr17-45839770-G-A
• rs242947
• ENST00000634876.2:n.603+3971C>T

Variant summary

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

The ENST00000634876.2(MAPT-AS1):​n.603+3971C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 152,114 control chromosomes in the GnomAD database, including 23,493 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 0.54 (23493 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000634876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466
• Publications: 10 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634876.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000634876.2	TSL:5	n.603+3971C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82643 AN: 151996 Hom.: 23488 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.814

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.543 AC: 82666 AN: 152114 Hom.: 23493 Cov.: 32 AF XY: 0.557 AC XY: 41396 AN XY: 74370

African (AFR) AF: 0.388 AC: 16098 AN: 41472

American (AMR) AF: 0.608 AC: 9288 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3472

East Asian (EAS) AF: 0.813 AC: 4195 AN: 5158

South Asian (SAS) AF: 0.767 AC: 3698 AN: 4822

European-Finnish (FIN) AF: 0.710 AC: 7523 AN: 10596

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38170 AN: 67998

Other (OTH) AF: 0.531 AC: 1123 AN: 2114

Alfa AF: 0.562 Hom.: 6298

Bravo AF: 0.528

Asia WGS AF: 0.749 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.31
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs242947; hg19: chr17-43917136;