chr1-99667734-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_017734.5(PALMD):c.219C>A(p.His73Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,613,402 control chromosomes in the GnomAD database, including 159 homozygotes. 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 Benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_017734.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PALMD | NM_017734.5 | c.219C>A | p.His73Gln | missense_variant | Exon 3 of 8 | ENST00000263174.9 | NP_060204.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PALMD | ENST00000263174.9 | c.219C>A | p.His73Gln | missense_variant | Exon 3 of 8 | 1 | NM_017734.5 | ENSP00000263174.4 | ||
PALMD | ENST00000605497.5 | c.219C>A | p.His73Gln | missense_variant | Exon 3 of 7 | 1 | ENSP00000473839.1 | |||
PALMD | ENST00000605613.1 | n.155C>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0179 AC: 2726AN: 152054Hom.: 75 Cov.: 32
GnomAD3 exomes AF: 0.00492 AC: 1235AN: 251018Hom.: 31 AF XY: 0.00363 AC XY: 492AN XY: 135640
GnomAD4 exome AF: 0.00198 AC: 2888AN: 1461232Hom.: 82 Cov.: 30 AF XY: 0.00180 AC XY: 1306AN XY: 726904
GnomAD4 genome AF: 0.0181 AC: 2748AN: 152170Hom.: 77 Cov.: 32 AF XY: 0.0176 AC XY: 1309AN XY: 74394
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at