19-42906951-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001031850.4(PSG6):āc.1211T>Gā(p.Ile404Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.004 in 1,612,242 control chromosomes in the GnomAD database, including 172 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001031850.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PSG6 | NM_001031850.4 | c.1211T>G | p.Ile404Ser | missense_variant | 5/6 | ENST00000187910.7 | |
PSG6 | NM_002782.5 | c.1211T>G | p.Ile404Ser | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PSG6 | ENST00000187910.7 | c.1211T>G | p.Ile404Ser | missense_variant | 5/6 | 1 | NM_001031850.4 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00380 AC: 576AN: 151432Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00431 AC: 1082AN: 250988Hom.: 31 AF XY: 0.00443 AC XY: 601AN XY: 135628
GnomAD4 exome AF: 0.00402 AC: 5874AN: 1460692Hom.: 164 Cov.: 32 AF XY: 0.00415 AC XY: 3013AN XY: 726636
GnomAD4 genome AF: 0.00381 AC: 578AN: 151550Hom.: 8 Cov.: 32 AF XY: 0.00374 AC XY: 277AN XY: 74060
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 | PSG6: BP4, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at