rs242928

Positions:

• chr17-45865685-G-A

Variant summary

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

The NR_024559.1(MAPT-AS1):​n.35-21524C>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 0.443 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 NR_024559.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-21524C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000634876.2	n.183-21524C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.423

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.438

Gnomad4 OTH AF: 0.437

Alfa AF: 0.437 Hom.: 10167

Bravo AF: 0.434

Asia WGS AF: 0.381 AC: 1327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242928; hg19: chr17-43943051;