rs4616318

Positions:

• chr17-45851444-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MAPT-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.35-7283T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.903-7283T>C		intron_variant		1
MAPT-AS1	ENST00000579244.1	n.122-7283T>C		intron_variant		2
MAPT-AS1	ENST00000634876.2	n.183-7283T>C		intron_variant		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

Gnomad4 AFR AF: 0.413

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.199

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.425

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4616318; hg19: chr17-43928810;