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rs9891103

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001377265.1(MAPT):c.2173+196C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,060 control chromosomes in the GnomAD database, including 4,503 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.23 ( 4503 hom., cov: 32)

Consequence

MAPT
NM_001377265.1 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.274
Variant links:
Genes affected
MAPT (HGNC:6893): (microtubule associated protein tau) This gene encodes the microtubule-associated protein tau (MAPT) whose transcript undergoes complex, regulated alternative splicing, giving rise to several mRNA species. MAPT transcripts are differentially expressed in the nervous system, depending on stage of neuronal maturation and neuron type. MAPT gene mutations have been associated with several neurodegenerative disorders such as Alzheimer's disease, Pick's disease, frontotemporal dementia, cortico-basal degeneration and progressive supranuclear palsy. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
Variant 17-46014520-C-T is Benign according to our data. Variant chr17-46014520-C-T is described in ClinVar as [Benign]. Clinvar id is 1225942.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
MAPTNM_001377265.1 linkuse as main transcriptc.2173+196C>T intron_variant ENST00000262410.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
MAPTENST00000262410.10 linkuse as main transcriptc.2173+196C>T intron_variant 1 NM_001377265.1 A2

Frequencies

GnomAD3 genomes
AF:
0.228
AC:
34638
AN:
151942
Hom.:
4507
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.324
Gnomad AMI
AF:
0.278
Gnomad AMR
AF:
0.212
Gnomad ASJ
AF:
0.251
Gnomad EAS
AF:
0.00154
Gnomad SAS
AF:
0.0816
Gnomad FIN
AF:
0.0668
Gnomad MID
AF:
0.280
Gnomad NFE
AF:
0.223
Gnomad OTH
AF:
0.255
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.228
AC:
34645
AN:
152060
Hom.:
4503
Cov.:
32
AF XY:
0.216
AC XY:
16086
AN XY:
74348
show subpopulations
Gnomad4 AFR
AF:
0.323
Gnomad4 AMR
AF:
0.211
Gnomad4 ASJ
AF:
0.251
Gnomad4 EAS
AF:
0.00155
Gnomad4 SAS
AF:
0.0814
Gnomad4 FIN
AF:
0.0668
Gnomad4 NFE
AF:
0.223
Gnomad4 OTH
AF:
0.251
Alfa
AF:
0.222
Hom.:
921
Bravo
AF:
0.244
Asia WGS
AF:
0.0440
AC:
157
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 03, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
Cadd
Benign
4.9
Dann
Benign
0.57

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9891103; hg19: chr17-44091886; COSMIC: COSV52247441; API