2-219628517-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005070.4(SLC4A3):c.164C>T(p.Pro55Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,364 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005070.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152054Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249538Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135222
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461310Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 726974
GnomAD4 genome AF: 0.000158 AC: 24AN: 152054Hom.: 1 Cov.: 31 AF XY: 0.000188 AC XY: 14AN XY: 74276
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.164C>T (p.P55L) alteration is located in exon 3 (coding exon 2) of the SLC4A3 gene. This alteration results from a C to T substitution at nucleotide position 164, causing the proline (P) at amino acid position 55 to be replaced by a leucine (L). 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