chr6-133241739-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004100.5(EYA4):c.-76C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0373 in 152,498 control chromosomes in the GnomAD database, including 377 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_004100.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EYA4 | NM_004100.5 | c.-76C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 20 | ENST00000355286.12 | NP_004091.3 | ||
EYA4 | NM_004100.5 | c.-76C>T | 5_prime_UTR_variant | Exon 1 of 20 | ENST00000355286.12 | NP_004091.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EYA4 | ENST00000355286 | c.-76C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 20 | 1 | NM_004100.5 | ENSP00000347434.7 | |||
EYA4 | ENST00000355286 | c.-76C>T | 5_prime_UTR_variant | Exon 1 of 20 | 1 | NM_004100.5 | ENSP00000347434.7 |
Frequencies
GnomAD3 genomes AF: 0.0373 AC: 5677AN: 152158Hom.: 376 Cov.: 33
GnomAD4 exome AF: 0.00893 AC: 2AN: 224Hom.: 0 Cov.: 0 AF XY: 0.0109 AC XY: 2AN XY: 184
GnomAD4 genome AF: 0.0373 AC: 5680AN: 152274Hom.: 377 Cov.: 33 AF XY: 0.0341 AC XY: 2542AN XY: 74462
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1J Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Autosomal dominant nonsyndromic hearing loss 10 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at