rs4792825

Positions:

• chr17-45842315-A-G
• chr17-45842315-A-T

Variant summary

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

The ENST00000634876.2(MAPT-AS1):​n.603+1426T>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 0.103 in 152,294 control chromosomes in the GnomAD database, including 904 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 0.10 (904 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000634876.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.116

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAPT-AS1	ENST00000634876.2	n.603+1426T>C		intron_variant, non_coding_transcript_variant		5
MAPT-AS1	ENST00000649665.1	n.2236T>C		non_coding_transcript_exon_variant	3/3
MAPT-AS1	ENST00000653949.1	n.1993T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15694 AN: 152176 Hom.: 903 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.0678

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0275

Gnomad FIN AF: 0.0751

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.0965

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

GnomAD4 genome AF: 0.103 AC: 15704 AN: 152294 Hom.: 904 Cov.: 32 AF XY: 0.0992 AC XY: 7385 AN XY: 74476

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.0677

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0275

Gnomad4 FIN AF: 0.0751

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.0955

Alfa AF: 0.106 Hom.: 299

Bravo AF: 0.103

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4792825; hg19: chr17-43919681;