17-45861104-A-G

Position:

• chr17-45861104-A-G

Variant summary

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

The NR_024559.1(MAPT-AS1):​n.35-16943T>C 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 0.675 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 NR_024559.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.712 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-16943T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000634876.2	n.183-16943T>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.650

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.435

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.682

Alfa AF: 0.695 Hom.: 24440

Bravo AF: 0.676

Asia WGS AF: 0.557 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs242933; hg19: chr17-43938470;