rs6480320
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_145178.4(ATOH7):c.-234C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0444 in 211,474 control chromosomes in the GnomAD database, including 947 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.060 ( 928 hom., cov: 33)
Exomes 𝑓: 0.0054 ( 19 hom. )
Consequence
ATOH7
NM_145178.4 5_prime_UTR
NM_145178.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.633
Genes affected
ATOH7 (HGNC:13907): (atonal bHLH transcription factor 7) This intronless gene encodes a member of the basic helix-loop-helix family of transcription factors, with similarity to Drosophila atonal gene that controls photoreceptor development. Studies in mice suggest that this gene plays a central role in retinal ganglion cell and optic nerve formation. Mutations in this gene are associated with nonsyndromic congenital retinal nonattachment. [provided by RefSeq, Dec 2011]
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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 10-68231911-G-A is Benign according to our data. Variant chr10-68231911-G-A is described in ClinVar as [Benign]. Clinvar id is 1254659.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATOH7 | NM_145178.4 | c.-234C>T | 5_prime_UTR_variant | 1/1 | ENST00000373673.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATOH7 | ENST00000373673.5 | c.-234C>T | 5_prime_UTR_variant | 1/1 | NM_145178.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0595 AC: 9056AN: 152164Hom.: 926 Cov.: 33
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GnomAD4 exome AF: 0.00536 AC: 317AN: 59192Hom.: 19 Cov.: 3 AF XY: 0.00456 AC XY: 138AN XY: 30296
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GnomAD4 genome ? AF: 0.0596 AC: 9076AN: 152282Hom.: 928 Cov.: 33 AF XY: 0.0568 AC XY: 4230AN XY: 74482
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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 | May 20, 2021 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at