17-45859044-T-C

Variant names:

• chr17-45859044-T-C
• rs242935
• ENST00000579599.1:n.903-14883A>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.903-14883A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,802 control chromosomes in the GnomAD database, including 27,483 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 0.59 (27483 hom., cov: 31)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-14883A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.903-14883A>G		intron_variant	Intron 1 of 1	1
MAPT-AS1	ENST00000579244.1	n.122-14883A>G		intron_variant	Intron 1 of 1	2
MAPT-AS1	ENST00000634876.2	n.183-14883A>G		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90212 AN: 151684 Hom.: 27469 Cov.: 31

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.627

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

GnomAD4 genome AF: 0.595 AC: 90264 AN: 151802 Hom.: 27483 Cov.: 31 AF XY: 0.591 AC XY: 43845 AN XY: 74170

African (AFR) AF: 0.496 AC: 20495 AN: 41362

American (AMR) AF: 0.664 AC: 10142 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2309 AN: 3464

East Asian (EAS) AF: 0.295 AC: 1517 AN: 5148

South Asian (SAS) AF: 0.513 AC: 2456 AN: 4790

European-Finnish (FIN) AF: 0.618 AC: 6509 AN: 10536

Middle Eastern (MID) AF: 0.670 AC: 197 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44620 AN: 67924

Other (OTH) AF: 0.624 AC: 1314 AN: 2106

Alfa AF: 0.616 Hom.: 3615

Bravo AF: 0.591

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs242935; hg19: chr17-43936410;