chr6-31864752-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_025257.3(SLC44A4):c.1927-16G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,880 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 Uncertain significance (★).
Frequency
Consequence
NM_025257.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC44A4 | NM_025257.3 | c.1927-16G>A | intron_variant | Intron 19 of 20 | ENST00000229729.11 | NP_079533.2 | ||
SLC44A4 | NM_001178044.2 | c.1801-16G>A | intron_variant | Intron 18 of 19 | NP_001171515.1 | |||
SLC44A4 | NM_001178045.2 | c.1699-16G>A | intron_variant | Intron 19 of 20 | NP_001171516.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC44A4 | ENST00000229729.11 | c.1927-16G>A | intron_variant | Intron 19 of 20 | 1 | NM_025257.3 | ENSP00000229729.6 | |||
SLC44A4 | ENST00000375562.8 | c.1801-16G>A | intron_variant | Intron 18 of 19 | 2 | ENSP00000364712.4 | ||||
SLC44A4 | ENST00000544672.5 | c.1699-16G>A | intron_variant | Intron 19 of 20 | 2 | ENSP00000444109.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251304Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135854
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461842Hom.: 0 Cov.: 34 AF XY: 0.0000413 AC XY: 30AN XY: 727222
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74270
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change falls in intron 19 of the SLC44A4 gene. It does not directly change the encoded amino acid sequence of the SLC44A4 protein. This variant is present in population databases (rs759785728, ExAC 0.02%). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with SLC44A4-related conditions. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at