12-30963941-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001370302.1(TSPAN11):c.200C>T(p.Ala67Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000347 in 1,614,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001370302.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TSPAN11 | NM_001370302.1 | c.200C>T | p.Ala67Val | missense_variant | Exon 3 of 8 | ENST00000546076.6 | NP_001357231.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TSPAN11 | ENST00000546076.6 | c.200C>T | p.Ala67Val | missense_variant | Exon 3 of 8 | 2 | NM_001370302.1 | ENSP00000437403.1 | ||
TSPAN11 | ENST00000261177.10 | c.200C>T | p.Ala67Val | missense_variant | Exon 3 of 8 | 1 | ENSP00000261177.9 | |||
TSPAN11 | ENST00000535215 | c.-14C>T | 5_prime_UTR_variant | Exon 2 of 7 | 2 | ENSP00000445503.1 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251342Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135854
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461710Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727186
GnomAD4 genome AF: 0.000118 AC: 18AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.200C>T (p.A67V) alteration is located in exon 3 (coding exon 2) of the TSPAN11 gene. This alteration results from a C to T substitution at nucleotide position 200, causing the alanine (A) at amino acid position 67 to be replaced by a valine (V). 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