chr11-93187236-C-T
Position:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_152313.4(SLC36A4):c.56-1422G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0125 in 152,160 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.013 ( 38 hom., cov: 32)
Consequence
SLC36A4
NM_152313.4 intron
NM_152313.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.158
Genes affected
SLC36A4 (HGNC:19660): (solute carrier family 36 member 4) SLC36A4 belongs to the SLC36 family of amino acid transporters based on sequence similarity with other family members (e.g., SLC36A1; MIM 606561). SLC36 proteins contain about 500 amino acids and have 9 to 11 transmembrane domains. Unlike other SLC36 family members, which are proton-coupled amino acid transporters, SLC36A4 is a high-affinity/low-capacity non-proton-coupled amino acid transporter (Pillai and Meredith, 2011 [PubMed 21097500]).[supplied by OMIM, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0125 (1907/152160) while in subpopulation AFR AF= 0.0434 (1801/41514). AF 95% confidence interval is 0.0417. There are 38 homozygotes in gnomad4. There are 908 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 38 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC36A4 | NM_152313.4 | c.56-1422G>A | intron_variant | ENST00000326402.9 | |||
SLC36A4 | NM_001286139.2 | c.-321-1422G>A | intron_variant | ||||
SLC36A4 | XM_047426350.1 | c.-2-1422G>A | intron_variant | ||||
SLC36A4 | XM_047426352.1 | c.56-1422G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC36A4 | ENST00000326402.9 | c.56-1422G>A | intron_variant | 1 | NM_152313.4 | P1 | |||
SLC36A4 | ENST00000529184.5 | c.-321-1422G>A | intron_variant | 2 | |||||
SLC36A4 | ENST00000524875.1 | c.56-1422G>A | intron_variant, NMD_transcript_variant | 3 | |||||
SLC36A4 | ENST00000527743.1 | n.153-1422G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0123 AC: 1876AN: 152042Hom.: 33 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0125 AC: 1907AN: 152160Hom.: 38 Cov.: 32 AF XY: 0.0122 AC XY: 908AN XY: 74406
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at