ENST00000649665.1:n.943A>G

Variant names:

• chr17-45843608-T-C
• rs17690326
• ENST00000649665.1:n.943A>G

Variant summary

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

The ENST00000649665.1(MAPT-AS1):​n.943A>G 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 0.143 in 152,238 control chromosomes in the GnomAD database, including 2,145 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 0.14 (2144 hom., cov: 32)
  • Exomes 𝑓: 0.19 (1 hom.)
• Consequence: MAPT-AS1 ENST00000649665.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.10
• Publications: 24 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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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
	MAPT-AS1	NR_024559.1		n.588A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAPT-AS1	ENST00000649665.1		n.943A>G		non_coding_transcript_exon	Exon 3 of 3
	MAPT-AS1	ENST00000653949.2		n.779A>G		non_coding_transcript_exon	Exon 2 of 2
	MAPT-AS1	ENST00000634876.2	TSL:5	n.603+133A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21834 AN: 152068 Hom.: 2146 Cov.: 32

Gnomad AFR AF: 0.0429

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.0651

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.186

GnomAD4 exome AF: 0.192 AC: 10 AN: 52 Hom.: 1 Cov.: 0 AF XY: 0.139 AC XY: 5 AN XY: 36

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.235 AC: 8 AN: 34

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.143 AC: 21824 AN: 152186 Hom.: 2144 Cov.: 32 AF XY: 0.134 AC XY: 9992 AN XY: 74424

African (AFR) AF: 0.0428 AC: 1778 AN: 41538

American (AMR) AF: 0.176 AC: 2689 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 836 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5174

South Asian (SAS) AF: 0.0739 AC: 356 AN: 4816

European-Finnish (FIN) AF: 0.0651 AC: 690 AN: 10606

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14763 AN: 67974

Other (OTH) AF: 0.183 AC: 387 AN: 2116

Alfa AF: 0.196 Hom.: 1319

Bravo AF: 0.148

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.77
DANN	Benign	0.46
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17690326; hg19: chr17-43920974;