rs7210728

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

MAPT-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAPT-AS1	NR_024559.1	n.34+4431C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAPT-AS1	ENST00000579599.1	n.902+3563C>T		intron_variant		1
MAPT-AS1	ENST00000579244.1	n.121+4431C>T		intron_variant		2
MAPT-AS1	ENST00000634876.2	n.182+4431C>T		intron_variant		5

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

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.131

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.335

Gnomad4 OTH AF: 0.298

Alfa AF: 0.323 Hom.: 9891

Bravo AF: 0.291

Asia WGS AF: 0.0880 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7210728; hg19: chr17-43968415;