chr6-26234549-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005320.3(H1-3):c.385C>T(p.Pro129Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,612,340 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_005320.3 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 |
---|---|---|---|---|---|---|---|
H1-3 | NM_005320.3 | c.385C>T | p.Pro129Ser | missense_variant | 1/1 | ENST00000244534.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
H1-3 | ENST00000244534.7 | c.385C>T | p.Pro129Ser | missense_variant | 1/1 | NM_005320.3 | P1 | ||
ENST00000707189.1 | n.999+110378G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1000+76428G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249218Hom.: 0 AF XY: 0.0000740 AC XY: 10AN XY: 135130
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1460330Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 726522
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 31, 2023 | The c.385C>T (p.P129S) alteration is located in exon 1 (coding exon 1) of the HIST1H1D gene. This alteration results from a C to T substitution at nucleotide position 385, causing the proline (P) at amino acid position 129 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