17-45847931-C-T

Variant names:

• chr17-45847931-C-T
• rs17690703
• ENST00000579599.1:n.903-3770G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579599.1(MAPT-AS1):​n.903-3770G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,108 control chromosomes in the GnomAD database, including 2,966 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 0.18 (2966 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 84 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=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.251 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-3770G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.903-3770G>A		intron_variant	Intron 1 of 1	1
MAPT-AS1	ENST00000579244.1	n.122-3770G>A		intron_variant	Intron 1 of 1	2
MAPT-AS1	ENST00000634876.2	n.183-3770G>A		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.176 AC: 26825 AN: 151990 Hom.: 2965 Cov.: 32

Gnomad AFR AF: 0.0713

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.0654

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.176 AC: 26827 AN: 152108 Hom.: 2966 Cov.: 32 AF XY: 0.166 AC XY: 12381 AN XY: 74372

African (AFR) AF: 0.0713 AC: 2961 AN: 41502

American (AMR) AF: 0.197 AC: 3015 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.256 AC: 889 AN: 3470

East Asian (EAS) AF: 0.0657 AC: 340 AN: 5174

South Asian (SAS) AF: 0.105 AC: 508 AN: 4816

European-Finnish (FIN) AF: 0.105 AC: 1109 AN: 10596

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17241 AN: 67954

Other (OTH) AF: 0.210 AC: 441 AN: 2098

Alfa AF: 0.218 Hom.: 6179

Bravo AF: 0.180

Asia WGS AF: 0.0870 AC: 304 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.8
DANN	Benign	0.73
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs17690703; hg19: chr17-43925297;