chr12-80937695-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004664.4(LIN7A):c.28C>T(p.Pro10Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000206 in 1,550,110 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 Uncertain significance (★).
Frequency
Consequence
NM_004664.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LIN7A | NM_004664.4 | c.28C>T | p.Pro10Ser | missense_variant | 1/6 | ENST00000552864.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LIN7A | ENST00000552864.6 | c.28C>T | p.Pro10Ser | missense_variant | 1/6 | 1 | NM_004664.4 | P1 | |
LIN7A | ENST00000549417.5 | c.10C>T | p.Pro4Ser | missense_variant | 1/5 | 1 | |||
LIN7A | ENST00000261203.7 | c.28C>T | p.Pro10Ser | missense_variant, NMD_transcript_variant | 1/7 | 1 | |||
ACSS3 | ENST00000616449.1 | n.1282G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00000661 AC: 1AN: 151344Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000413 AC: 9AN: 218024Hom.: 0 AF XY: 0.0000503 AC XY: 6AN XY: 119340
GnomAD4 exome AF: 0.0000222 AC: 31AN: 1398766Hom.: 0 Cov.: 32 AF XY: 0.0000273 AC XY: 19AN XY: 694704
GnomAD4 genome AF: 0.00000661 AC: 1AN: 151344Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 73816
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2023 | The c.28C>T (p.P10S) alteration is located in exon 1 (coding exon 1) of the LIN7A gene. This alteration results from a C to T substitution at nucleotide position 28, causing the proline (P) at amino acid position 10 to be replaced by a serine (S). 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