rs1109166
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_005072.5(SLC12A4):c.*1361A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 528,266 control chromosomes in the GnomAD database, including 20,265 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005072.5 3_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC12A4 | NM_005072.5 | c.*1361A>G | 3_prime_UTR_variant | Exon 24 of 24 | ENST00000316341.8 | NP_005063.1 | ||
LCAT | NM_000229.2 | c.155-267A>G | intron_variant | Intron 1 of 5 | ENST00000264005.10 | NP_000220.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC12A4 | ENST00000316341 | c.*1361A>G | 3_prime_UTR_variant | Exon 24 of 24 | 1 | NM_005072.5 | ENSP00000318557.3 | |||
LCAT | ENST00000264005.10 | c.155-267A>G | intron_variant | Intron 1 of 5 | 1 | NM_000229.2 | ENSP00000264005.5 | |||
LCAT | ENST00000570980.1 | c.-329A>G | 5_prime_UTR_variant | Exon 1 of 5 | 2 | ENSP00000464651.1 | ||||
LCAT | ENST00000575467.5 | n.155-290A>G | intron_variant | Intron 1 of 5 | 5 | ENSP00000460653.1 |
Frequencies
GnomAD3 genomes AF: 0.316 AC: 47984AN: 151972Hom.: 10968 Cov.: 33
GnomAD4 exome AF: 0.200 AC: 75377AN: 376176Hom.: 9262 Cov.: 0 AF XY: 0.201 AC XY: 39969AN XY: 199076
GnomAD4 genome AF: 0.316 AC: 48074AN: 152090Hom.: 11003 Cov.: 33 AF XY: 0.314 AC XY: 23334AN XY: 74360
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is associated with the following publications: (PMID: 31039173, 25814643) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at