20-31639921-TTG-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_032609.3(COX4I2):c.83-8_83-7delGT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0075 in 1,613,788 control chromosomes in the GnomAD database, including 72 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_032609.3 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COX4I2 | NM_032609.3 | c.83-8_83-7delGT | splice_region_variant, intron_variant | Intron 2 of 4 | ENST00000376075.4 | NP_115998.2 | ||
COX4I2 | XM_005260579.5 | c.98-8_98-7delGT | splice_region_variant, intron_variant | Intron 1 of 3 | XP_005260636.1 | |||
COX4I2 | XM_005260580.5 | c.98-8_98-7delGT | splice_region_variant, intron_variant | Intron 1 of 2 | XP_005260637.1 | |||
COX4I2 | XM_005260581.4 | c.83-8_83-7delGT | splice_region_variant, intron_variant | Intron 2 of 3 | XP_005260638.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00481 AC: 731AN: 152082Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.00478 AC: 1201AN: 251034Hom.: 6 AF XY: 0.00494 AC XY: 671AN XY: 135716
GnomAD4 exome AF: 0.00778 AC: 11377AN: 1461588Hom.: 69 AF XY: 0.00770 AC XY: 5600AN XY: 727088
GnomAD4 genome AF: 0.00480 AC: 731AN: 152200Hom.: 3 Cov.: 31 AF XY: 0.00465 AC XY: 346AN XY: 74402
ClinVar
Submissions by phenotype
not provided Benign:3
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COX4I2: BP4, BS2 -
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Pancreatic insufficiency-anemia-hyperostosis syndrome Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at