17-45849423-T-C

Variant names:

• chr17-45849423-T-C
• rs8064870
• ENST00000579599.1:n.903-5262A>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.903-5262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,016 control chromosomes in the GnomAD database, including 11,343 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 0.38 (11343 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529
• Publications: 22 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579599.1. 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
	MAPT-AS1	NR_024559.1		n.35-5262A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000579599.1	TSL:1	n.903-5262A>G		intron	N/A
	MAPT-AS1	ENST00000579244.1	TSL:2	n.122-5262A>G		intron	N/A
	MAPT-AS1	ENST00000634876.2	TSL:5	n.183-5262A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57097 AN: 151898 Hom.: 11334 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.376 AC: 57133 AN: 152016 Hom.: 11343 Cov.: 32 AF XY: 0.365 AC XY: 27117 AN XY: 74300

African (AFR) AF: 0.285 AC: 11825 AN: 41464

American (AMR) AF: 0.372 AC: 5683 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1525 AN: 3470

East Asian (EAS) AF: 0.188 AC: 968 AN: 5150

South Asian (SAS) AF: 0.297 AC: 1435 AN: 4826

European-Finnish (FIN) AF: 0.282 AC: 2986 AN: 10588

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31280 AN: 67910

Other (OTH) AF: 0.401 AC: 847 AN: 2112

Alfa AF: 0.435 Hom.: 16046

Bravo AF: 0.379

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.73
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs8064870; hg19: chr17-43926789;