rs5015
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_000342.4(SLC4A1):c.1249C>T(p.Leu417Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 1,614,124 control chromosomes in the GnomAD database, including 1,543 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000342.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC4A1 | NM_000342.4 | c.1249C>T | p.Leu417Leu | synonymous_variant | Exon 11 of 20 | ENST00000262418.12 | NP_000333.1 | |
SLC4A1 | XM_011525129.3 | c.1249C>T | p.Leu417Leu | synonymous_variant | Exon 11 of 19 | XP_011523431.1 | ||
SLC4A1 | XM_005257593.6 | c.1054C>T | p.Leu352Leu | synonymous_variant | Exon 9 of 18 | XP_005257650.1 | ||
SLC4A1 | XM_011525130.2 | c.1249C>T | p.Leu417Leu | synonymous_variant | Exon 11 of 18 | XP_011523432.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC4A1 | ENST00000262418.12 | c.1249C>T | p.Leu417Leu | synonymous_variant | Exon 11 of 20 | 1 | NM_000342.4 | ENSP00000262418.6 | ||
SLC4A1 | ENST00000399246.3 | c.777+1243C>T | intron_variant | Intron 9 of 14 | 5 | ENSP00000382190.3 |
Frequencies
GnomAD3 genomes AF: 0.0306 AC: 4661AN: 152144Hom.: 89 Cov.: 31
GnomAD3 exomes AF: 0.0334 AC: 8404AN: 251372Hom.: 181 AF XY: 0.0350 AC XY: 4753AN XY: 135878
GnomAD4 exome AF: 0.0418 AC: 61086AN: 1461862Hom.: 1454 Cov.: 33 AF XY: 0.0417 AC XY: 30326AN XY: 727244
GnomAD4 genome AF: 0.0306 AC: 4656AN: 152262Hom.: 89 Cov.: 31 AF XY: 0.0300 AC XY: 2231AN XY: 74440
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:4
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Autosomal dominant distal renal tubular acidosis Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Hereditary spherocytosis type 4 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Hemolytic anemia Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at