NM_001080476.3:c.628-9C>A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate
The NM_001080476.3(GRXCR1):c.628-9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000214 in 1,587,308 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001080476.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 249010Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135102
GnomAD4 exome AF: 0.0000202 AC: 29AN: 1435124Hom.: 0 Cov.: 27 AF XY: 0.0000168 AC XY: 12AN XY: 715814
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not provided Pathogenic:1
This sequence change falls in intron 2 of the GRXCR1 gene. It does not directly change the encoded amino acid sequence of the GRXCR1 protein. This variant is present in population databases (rs606231120, gnomAD 0.002%). This variant has been observed in individual(s) with autosomal recessive deafness (PMID: 20137778). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 193). Studies have shown that this variant is associated with altered splicing resulting in unknown protein product impact (PMID: 20137778). For these reasons, this variant has been classified as Pathogenic. -
Autosomal recessive nonsyndromic hearing loss 25 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at