chrX-124384061-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_001163278.2(TENM1):c.6870G>A(p.Leu2290Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00036 in 1,209,764 control chromosomes in the GnomAD database, including 2 homozygotes. There are 108 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001163278.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TENM1 | NM_001163278.2 | c.6870G>A | p.Leu2290Leu | synonymous_variant | Exon 33 of 35 | NP_001156750.1 | ||
TENM1 | NM_001163279.1 | c.6867G>A | p.Leu2289Leu | synonymous_variant | Exon 30 of 32 | NP_001156751.1 | ||
TENM1 | NM_014253.3 | c.6849G>A | p.Leu2283Leu | synonymous_variant | Exon 29 of 31 | NP_055068.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TENM1 | ENST00000371130.7 | c.6849G>A | p.Leu2283Leu | synonymous_variant | Exon 29 of 31 | 1 | ENSP00000360171.3 | |||
TENM1 | ENST00000422452.3 | c.6816G>A | p.Leu2272Leu | synonymous_variant | Exon 33 of 35 | 1 | ENSP00000403954.4 | |||
STAG2 | ENST00000469481.1 | n.454-27761C>T | intron_variant | Intron 2 of 3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00209 AC: 234AN: 111696Hom.: 0 Cov.: 22 AF XY: 0.00177 AC XY: 60AN XY: 33872
GnomAD3 exomes AF: 0.000553 AC: 101AN: 182648Hom.: 0 AF XY: 0.000445 AC XY: 30AN XY: 67410
GnomAD4 exome AF: 0.000183 AC: 201AN: 1098017Hom.: 2 Cov.: 32 AF XY: 0.000132 AC XY: 48AN XY: 363395
GnomAD4 genome AF: 0.00209 AC: 234AN: 111747Hom.: 0 Cov.: 22 AF XY: 0.00177 AC XY: 60AN XY: 33933
ClinVar
Submissions by phenotype
TENM1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at