chr6-26199096-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003530.4(H3C4):c.-257G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000809 in 1,614,178 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003530.4 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
H2AC7 | NM_021065.3 | c.148G>T | p.Val50Leu | missense_variant | Exon 1 of 1 | ENST00000341023.2 | NP_066409.1 | |
H3C4 | NM_003530.4 | c.-257G>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 2 | NP_003521.2 | |||
H3C4 | NM_003530.4 | c.-257G>T | 5_prime_UTR_variant | Exon 1 of 2 | NP_003521.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
H2AC7 | ENST00000341023.2 | c.148G>T | p.Val50Leu | missense_variant | Exon 1 of 1 | 6 | NM_021065.3 | ENSP00000341094.2 | ||
ENSG00000282988 | ENST00000635200.1 | c.148G>T | p.Val50Leu | missense_variant | Exon 1 of 2 | 3 | ENSP00000489311.1 |
Frequencies
GnomAD3 genomes AF: 0.000591 AC: 90AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000570 AC: 143AN: 250668Hom.: 1 AF XY: 0.000656 AC XY: 89AN XY: 135720
GnomAD4 exome AF: 0.000833 AC: 1217AN: 1461822Hom.: 4 Cov.: 32 AF XY: 0.000861 AC XY: 626AN XY: 727224
GnomAD4 genome AF: 0.000584 AC: 89AN: 152356Hom.: 0 Cov.: 33 AF XY: 0.000617 AC XY: 46AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.148G>T (p.V50L) alteration is located in exon 1 (coding exon 1) of the HIST1H2AD gene. This alteration results from a G to T substitution at nucleotide position 148, causing the valine (V) at amino acid position 50 to be replaced by a leucine (L). 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