rs7210728

Variant names:

• chr17-45891049-G-A
• rs7210728
• ENST00000579599.1:n.902+3563C>T

Your query was ambiguous. Multiple possible variants found:

• chr17-45891049-G-A
• chr17-45891049-G-T

Variant summary

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

The ENST00000579599.1(MAPT-AS1):​n.902+3563C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,026 control chromosomes in the GnomAD database, including 6,674 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 0.29 (6674 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 28 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000579599.1. 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
	MAPT-AS1	NR_024559.1		n.34+4431C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000579599.1	TSL:1	n.902+3563C>T		intron	N/A
	MAPT-AS1	ENST00000579244.1	TSL:2	n.121+4431C>T		intron	N/A
	MAPT-AS1	ENST00000634876.2	TSL:5	n.182+4431C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43465 AN: 151908 Hom.: 6672 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.258

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.286 AC: 43484 AN: 152026 Hom.: 6674 Cov.: 32 AF XY: 0.276 AC XY: 20495 AN XY: 74314

African (AFR) AF: 0.277 AC: 11472 AN: 41456

American (AMR) AF: 0.258 AC: 3935 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3468

East Asian (EAS) AF: 0.0172 AC: 89 AN: 5182

South Asian (SAS) AF: 0.131 AC: 633 AN: 4826

European-Finnish (FIN) AF: 0.208 AC: 2189 AN: 10546

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22762 AN: 67978

Other (OTH) AF: 0.298 AC: 628 AN: 2108

Alfa AF: 0.316 Hom.: 27659

Bravo AF: 0.291

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.46
PhyloP100		0.0010

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7210728;

hg19: chr17-43968415;