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. The variant received -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
• Publications: 10 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649665.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000649665.1		n.2236T>C		non_coding_transcript_exon	Exon 3 of 3
	MAPT-AS1	ENST00000653949.2		n.2072T>C		non_coding_transcript_exon	Exon 2 of 2
	MAPT-AS1	ENST00000634876.2	TSL:5	n.603+1426T>C		intron	N/A

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

African (AFR) AF: 0.139 AC: 5788 AN: 41532

American (AMR) AF: 0.0677 AC: 1036 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 361 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0275 AC: 133 AN: 4830

European-Finnish (FIN) AF: 0.0751 AC: 798 AN: 10620

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7284 AN: 68024

Other (OTH) AF: 0.0955 AC: 202 AN: 2116

Alfa AF: 0.106 Hom.: 910

Bravo AF: 0.103

Asia WGS AF: 0.0210 AC: 74 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.1
DANN	Benign	0.51
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4792825; hg19: chr17-43919681;