rs5036
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000342.4(SLC4A1):āc.166A>Gā(p.Lys56Glu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 1,614,042 control chromosomes in the GnomAD database, including 1,705 homozygotes. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_000342.4 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC4A1 | NM_000342.4 | c.166A>G | p.Lys56Glu | missense_variant, splice_region_variant | 4/20 | ENST00000262418.12 | |
SLC4A1 | XM_011525129.3 | c.166A>G | p.Lys56Glu | missense_variant, splice_region_variant | 4/19 | ||
SLC4A1 | XM_011525130.2 | c.166A>G | p.Lys56Glu | missense_variant, splice_region_variant | 4/18 | ||
SLC4A1 | XM_005257593.6 | c.-30A>G | splice_region_variant, 5_prime_UTR_variant | 2/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC4A1 | ENST00000262418.12 | c.166A>G | p.Lys56Glu | missense_variant, splice_region_variant | 4/20 | 1 | NM_000342.4 | P1 | |
SLC4A1 | ENST00000399246.3 | c.166A>G | p.Lys56Glu | missense_variant, splice_region_variant | 4/15 | 5 | |||
SLC4A1 | ENST00000471005.5 | n.100A>G | splice_region_variant, non_coding_transcript_exon_variant | 2/4 | 3 | ||||
SLC4A1 | ENST00000498270.1 | n.447A>G | splice_region_variant, non_coding_transcript_exon_variant | 3/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0493 AC: 7503AN: 152094Hom.: 342 Cov.: 32
GnomAD3 exomes AF: 0.0446 AC: 11216AN: 251446Hom.: 512 AF XY: 0.0392 AC XY: 5324AN XY: 135904
GnomAD4 exome AF: 0.0306 AC: 44670AN: 1461830Hom.: 1363 Cov.: 32 AF XY: 0.0300 AC XY: 21796AN XY: 727224
GnomAD4 genome AF: 0.0494 AC: 7514AN: 152212Hom.: 342 Cov.: 32 AF XY: 0.0483 AC XY: 3591AN XY: 74424
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 03, 2020 | This variant is associated with the following publications: (PMID: 29396846, 1520883) - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 30, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Hereditary spherocytosis type 4 Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | - - |
Benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
BAND 3 MEMPHIS Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2009 | - - |
Autosomal dominant distal renal tubular acidosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | - - |
Hemolytic anemia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at