rs1248649998
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_005422.4(TECTA):c.1871C>T(p.Ala624Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000031 in 1,613,990 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_005422.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TECTA | NM_005422.4 | c.1871C>T | p.Ala624Val | missense_variant | 9/24 | ENST00000392793.6 | |
TBCEL-TECTA | NM_001378761.1 | c.2828C>T | p.Ala943Val | missense_variant | 15/30 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TECTA | ENST00000392793.6 | c.1871C>T | p.Ala624Val | missense_variant | 9/24 | 5 | NM_005422.4 | P4 | |
TECTA | ENST00000264037.2 | c.1871C>T | p.Ala624Val | missense_variant | 8/23 | 1 | P4 | ||
TECTA | ENST00000642222.1 | c.1871C>T | p.Ala624Val | missense_variant | 9/24 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250854Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135648
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461740Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727184
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74378
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 22, 2017 | p.Ala624Val in exon 8 of TECTA: This variant is not expected to have clinical si gnificance due to a lack of conservation across species, including mammals. Of n ote, four mammals (Tibetan antelope, cow, sheep, domestic goat) have a valine (V al) at this position despite high nearby amino acid conservation. It has also be en identified in 1/33566 Latino chromosomes by the Genome Aggregation Database ( gnomAD, http://gnomad.broadinstitute.org) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at