chr3-190312890-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PP3_ModerateBP6_Very_StrongBS2
The NM_021101.5(CLDN1):c.370G>A(p.Ala124Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00337 in 1,613,992 control chromosomes in the GnomAD database, including 33 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A124V) has been classified as Likely benign.
Frequency
Consequence
NM_021101.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLDN1 | NM_021101.5 | c.370G>A | p.Ala124Thr | missense_variant | 2/4 | ENST00000295522.4 | |
CLDN16 | NM_001378492.1 | c.-445-2003C>T | intron_variant | ||||
CLDN16 | NM_001378493.1 | c.-279+22299C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN1 | ENST00000295522.4 | c.370G>A | p.Ala124Thr | missense_variant | 2/4 | 1 | NM_021101.5 | P1 | |
CLDN1 | ENST00000490800.1 | n.329G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00410 AC: 623AN: 152100Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00422 AC: 1061AN: 251422Hom.: 9 AF XY: 0.00399 AC XY: 542AN XY: 135870
GnomAD4 exome AF: 0.00329 AC: 4809AN: 1461774Hom.: 27 Cov.: 30 AF XY: 0.00324 AC XY: 2357AN XY: 727194
GnomAD4 genome AF: 0.00409 AC: 623AN: 152218Hom.: 6 Cov.: 33 AF XY: 0.00485 AC XY: 361AN XY: 74426
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | CLDN1: PP3, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at