chr11-93181731-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152313.4(SLC36A4):āc.415A>Gā(p.Ser139Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000816 in 1,543,910 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_152313.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC36A4 | NM_152313.4 | c.415A>G | p.Ser139Gly | missense_variant | 5/11 | ENST00000326402.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC36A4 | ENST00000326402.9 | c.415A>G | p.Ser139Gly | missense_variant | 5/11 | 1 | NM_152313.4 | P1 | |
SLC36A4 | ENST00000529184.5 | c.10A>G | p.Ser4Gly | missense_variant | 5/11 | 2 | |||
SLC36A4 | ENST00000534116.1 | c.97A>G | p.Ser33Gly | missense_variant | 2/7 | 3 | |||
SLC36A4 | ENST00000524875.1 | c.*50A>G | 3_prime_UTR_variant, NMD_transcript_variant | 5/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000395 AC: 60AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000109 AC: 18AN: 164884Hom.: 0 AF XY: 0.000114 AC XY: 10AN XY: 87508
GnomAD4 exome AF: 0.0000474 AC: 66AN: 1391856Hom.: 0 Cov.: 25 AF XY: 0.0000407 AC XY: 28AN XY: 687638
GnomAD4 genome AF: 0.000395 AC: 60AN: 152054Hom.: 0 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74270
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 12, 2023 | The c.415A>G (p.S139G) alteration is located in exon 5 (coding exon 5) of the SLC36A4 gene. This alteration results from a A to G substitution at nucleotide position 415, causing the serine (S) at amino acid position 139 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at