17-45849423-T-C

Position:

• chr17-45849423-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000579599.1(MAPT-AS1):​n.903-5262A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 152,016 control chromosomes in the GnomAD database, including 11,343 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 0.38 (11343 hom., cov: 32)
• Consequence: MAPT-AS1 ENST00000579599.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.529

Genes affected

MAPT-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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.35-5262A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.903-5262A>G		intron_variant		1
MAPT-AS1	ENST00000579244.1	n.122-5262A>G		intron_variant		2
MAPT-AS1	ENST00000634876.2	n.183-5262A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57097 AN: 151898 Hom.: 11334 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.376 AC: 57133 AN: 152016 Hom.: 11343 Cov.: 32 AF XY: 0.365 AC XY: 27117 AN XY: 74300

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.282

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.401

Alfa AF: 0.434 Hom.: 12969

Bravo AF: 0.379

Asia WGS AF: 0.250 AC: 870 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8064870; hg19: chr17-43926789;