rs4616318

Variant names:

• chr17-45851444-A-G
• rs4616318
• ENST00000579599.1:n.903-7283T>C

Variant summary

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

The ENST00000579599.1(MAPT-AS1):​n.903-7283T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 152,076 control chromosomes in the GnomAD database, including 13,280 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 0.41 (13280 hom., cov: 33)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530
• Publications: 9 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-7283T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.903-7283T>C		intron_variant	Intron 1 of 1	1
MAPT-AS1	ENST00000579244.1	n.122-7283T>C		intron_variant	Intron 1 of 1	2
MAPT-AS1	ENST00000634876.2	n.183-7283T>C		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62538 AN: 151958 Hom.: 13258 Cov.: 33

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.412 AC: 62605 AN: 152076 Hom.: 13280 Cov.: 33 AF XY: 0.399 AC XY: 29697 AN XY: 74352

African (AFR) AF: 0.413 AC: 17115 AN: 41464

American (AMR) AF: 0.379 AC: 5799 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1517 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1029 AN: 5172

South Asian (SAS) AF: 0.288 AC: 1390 AN: 4822

European-Finnish (FIN) AF: 0.282 AC: 2991 AN: 10598

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31281 AN: 67944

Other (OTH) AF: 0.425 AC: 898 AN: 2112

Alfa AF: 0.438 Hom.: 3031

Bravo AF: 0.421

Asia WGS AF: 0.266 AC: 925 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.62
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs4616318; hg19: chr17-43928810;