11-75606128-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The ENST00000304771.8(MAP6):c.1120-124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,138,626 control chromosomes in the GnomAD database, including 8,300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.086 ( 763 hom., cov: 32)
Exomes 𝑓: 0.12 ( 7537 hom. )
Consequence
MAP6
ENST00000304771.8 intron
ENST00000304771.8 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.971
Genes affected
MAP6 (HGNC:6868): (microtubule associated protein 6) This gene encodes a microtubule-associated protein. The encoded protein is a calmodulin-binding and calmodulin-regulated protein that is involved in microtubule stabilization. Two transcript variants encoding distinct isoforms have been identified for this gene. [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=-0.8).
BP6
Variant 11-75606128-G-A is Benign according to our data. Variant chr11-75606128-G-A is described in ClinVar as [Benign]. Clinvar id is 1270127.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP6 | NM_033063.2 | c.1120-124C>T | intron_variant | ENST00000304771.8 | NP_149052.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP6 | ENST00000304771.8 | c.1120-124C>T | intron_variant | 1 | NM_033063.2 | ENSP00000307093 | A2 | |||
MAP6 | ENST00000434603.2 | c.1120-124C>T | intron_variant | 1 | ENSP00000415108 | P2 | ||||
MAP6 | ENST00000526740.3 | c.133-124C>T | intron_variant | 5 | ENSP00000434278 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0856 AC: 13031AN: 152166Hom.: 766 Cov.: 32
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GnomAD4 exome AF: 0.118 AC: 116715AN: 986342Hom.: 7537 AF XY: 0.119 AC XY: 59165AN XY: 495476
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GnomAD4 genome AF: 0.0855 AC: 13027AN: 152284Hom.: 763 Cov.: 32 AF XY: 0.0858 AC XY: 6389AN XY: 74464
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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 submitter | clinical testing | GeneDx | Jun 20, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at