rs242947

Positions:

• chr17-45839770-G-A
• chr17-45839770-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000634876.2(MAPT-AS1):​n.603+3971C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.466

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPT-AS1	ENST00000634876.2	n.603+3971C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.710

Gnomad4 NFE AF: 0.561

Gnomad4 OTH AF: 0.531

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242947; hg19: chr17-43917136;