rs558080743
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PM4_SupportingBS2
The NM_001201543.2(FAM161A):c.2124_2126delAGA(p.Glu709del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000921 in 1,610,376 control chromosomes in the GnomAD database, including 4 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001201543.2 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000795 AC: 121AN: 152230Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000449 AC: 109AN: 242832Hom.: 0 AF XY: 0.000494 AC XY: 65AN XY: 131552
GnomAD4 exome AF: 0.000934 AC: 1362AN: 1458028Hom.: 2 AF XY: 0.000913 AC XY: 662AN XY: 724930
GnomAD4 genome AF: 0.000794 AC: 121AN: 152348Hom.: 2 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74492
ClinVar
Submissions by phenotype
Retinitis pigmentosa 28 Uncertain:1
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not provided Uncertain:1
This variant, c.2124_2126del, results in the deletion of 1 amino acid(s) of the FAM161A protein (p.Glu709del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs558080743, gnomAD 0.09%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with FAM161A-related conditions. ClinVar contains an entry for this variant (Variation ID: 553904). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Retinal dystrophy Uncertain:1
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Retinitis pigmentosa Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at