chr1-151895052-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_053055.5(THEM4):c.242G>A(p.Arg81His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00931 in 1,613,964 control chromosomes in the GnomAD database, including 81 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 (★★).
Frequency
Consequence
NM_053055.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THEM4 | ENST00000368814.8 | c.242G>A | p.Arg81His | missense_variant | Exon 2 of 6 | 1 | NM_053055.5 | ENSP00000357804.3 | ||
THEM4 | ENST00000471464.5 | n.242G>A | non_coding_transcript_exon_variant | Exon 2 of 7 | 1 | ENSP00000431288.1 | ||||
THEM4 | ENST00000489410.1 | c.242G>A | p.Arg81His | missense_variant | Exon 2 of 2 | 2 | ENSP00000433304.1 | |||
ENSG00000285651 | ENST00000648930.1 | n.32-1260C>T | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.00669 AC: 1017AN: 152014Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00748 AC: 1881AN: 251390Hom.: 18 AF XY: 0.00735 AC XY: 999AN XY: 135874
GnomAD4 exome AF: 0.00959 AC: 14014AN: 1461832Hom.: 75 Cov.: 29 AF XY: 0.00924 AC XY: 6716AN XY: 727212
GnomAD4 genome AF: 0.00668 AC: 1017AN: 152132Hom.: 6 Cov.: 32 AF XY: 0.00671 AC XY: 499AN XY: 74384
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