rs1078830

Variant names:

• chr17-45868746-T-C
• rs1078830
• ENST00000579599.1:n.903-24585A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-45868746-T-C
• chr17-45868746-T-G

Variant summary

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

The ENST00000579599.1(MAPT-AS1):​n.903-24585A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,246 control chromosomes in the GnomAD database, including 2,144 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)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.408
• Publications: 19 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-24585A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.903-24585A>G		intron_variant	Intron 1 of 1	1
MAPT-AS1	ENST00000579244.1	n.122-24585A>G		intron_variant	Intron 1 of 1	2
MAPT-AS1	ENST00000634876.2	n.183-24585A>G		intron_variant	Intron 1 of 6	5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21862 AN: 152128 Hom.: 2146 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.144 AC: 21852 AN: 152246 Hom.: 2144 Cov.: 32 AF XY: 0.134 AC XY: 9997 AN XY: 74444

African (AFR) AF: 0.0429 AC: 1782 AN: 41542

American (AMR) AF: 0.176 AC: 2692 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3470

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5184

South Asian (SAS) AF: 0.0738 AC: 356 AN: 4824

European-Finnish (FIN) AF: 0.0650 AC: 689 AN: 10606

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

European-Non Finnish (NFE) AF: 0.217 AC: 14786 AN: 68006

Other (OTH) AF: 0.183 AC: 387 AN: 2114

Alfa AF: 0.175 Hom.: 2206

Bravo AF: 0.148

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.7
DANN	Benign	0.34
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1078830; hg19: chr17-43946112;