17-45836178-G-T

Variant names:

• chr17-45836178-G-T
• rs242948
• ENST00000634876.2:n.604-6817C>A

Variant summary

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

The ENST00000634876.2(MAPT-AS1):​n.604-6817C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 152,002 control chromosomes in the GnomAD database, including 24,302 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 0.56 (24302 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000634876.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 11 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634876.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000634876.2	TSL:5	n.604-6817C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84534 AN: 151884 Hom.: 24298 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.561

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.556 AC: 84558 AN: 152002 Hom.: 24302 Cov.: 32 AF XY: 0.569 AC XY: 42290 AN XY: 74300

African (AFR) AF: 0.435 AC: 18036 AN: 41422

American (AMR) AF: 0.612 AC: 9350 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1876 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4162 AN: 5156

South Asian (SAS) AF: 0.768 AC: 3705 AN: 4822

European-Finnish (FIN) AF: 0.707 AC: 7485 AN: 10580

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.561 AC: 38107 AN: 67958

Other (OTH) AF: 0.540 AC: 1137 AN: 2106

Alfa AF: 0.431 Hom.: 1198

Bravo AF: 0.542

Asia WGS AF: 0.753 AC: 2618 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.75
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs242948; hg19: chr17-43913544;