rs4792825

Variant names:

• chr17-45842315-A-G
• rs4792825
• ENST00000649665.1:n.2236T>C

Your query was ambiguous. Multiple possible variants found:

• 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 ENST00000649665.1(MAPT-AS1):​n.2236T>C variant causes a non coding transcript exon 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 ENST00000649665.1 non_coding_transcript_exon
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000649665.1	n.2236T>C		non_coding_transcript_exon_variant	Exon 3 of 3
MAPT-AS1	ENST00000653949.1	n.1993T>C		non_coding_transcript_exon_variant	Exon 2 of 2
MAPT-AS1	ENST00000634876.2	n.603+1426T>C		intron_variant	Intron 2 of 6	5

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;