rs141768405
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_024809.5(TCTN2):c.-2G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000445 in 1,612,594 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_024809.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCTN2 | NM_024809.5 | c.-2G>A | 5_prime_UTR_variant | Exon 1 of 18 | ENST00000303372.7 | NP_079085.2 | ||
TCTN2 | NM_001143850.3 | c.-2G>A | 5_prime_UTR_variant | Exon 1 of 18 | NP_001137322.1 | |||
TCTN2 | NM_001410989.1 | c.-2G>A | 5_prime_UTR_variant | Exon 1 of 17 | NP_001397918.1 | |||
TCTN2 | XM_017019974.2 | c.-2G>A | 5_prime_UTR_variant | Exon 1 of 17 | XP_016875463.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00210 AC: 319AN: 152196Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000531 AC: 131AN: 246858Hom.: 0 AF XY: 0.000470 AC XY: 63AN XY: 134002
GnomAD4 exome AF: 0.000274 AC: 400AN: 1460280Hom.: 2 Cov.: 32 AF XY: 0.000268 AC XY: 195AN XY: 726410
GnomAD4 genome AF: 0.00208 AC: 317AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.00215 AC XY: 160AN XY: 74478
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
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See Variant Classification Assertion Criteria. -
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at