chr4-166003420-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_012464.5(TLL1):c.662A>G(p.Asn221Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_012464.5 missense
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TLL1 | NM_012464.5 | c.662A>G | p.Asn221Ser | missense_variant | 6/21 | ENST00000061240.7 | |
TLL1 | NM_001204760.2 | c.662A>G | p.Asn221Ser | missense_variant | 6/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TLL1 | ENST00000061240.7 | c.662A>G | p.Asn221Ser | missense_variant | 6/21 | 1 | NM_012464.5 | P1 | |
TLL1 | ENST00000507499.5 | c.662A>G | p.Asn221Ser | missense_variant | 6/22 | 1 | |||
TLL1 | ENST00000513213.5 | c.662A>G | p.Asn221Ser | missense_variant | 6/10 | 1 | |||
TLL1 | ENST00000509505.5 | c.*307A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/21 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000795 AC: 20AN: 251426Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135888
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727190
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74302
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | TLL1: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at