chr10-113567499-T-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004132.5(HABP2):āc.80T>Gā(p.Met27Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000158 in 1,460,222 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004132.5 missense
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HABP2 | NM_004132.5 | c.80T>G | p.Met27Arg | missense_variant | 2/13 | ENST00000351270.4 | NP_004123.1 | |
HABP2 | NM_001177660.3 | c.2T>G | p.Met1? | start_lost | 2/13 | NP_001171131.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HABP2 | ENST00000351270.4 | c.80T>G | p.Met27Arg | missense_variant | 2/13 | 1 | NM_004132.5 | ENSP00000277903 | P1 | |
HABP2 | ENST00000542051.5 | c.2T>G | p.Met1? | start_lost | 2/13 | 2 | ENSP00000443283 | |||
HABP2 | ENST00000460714.1 | n.16T>G | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251374Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135854
GnomAD4 exome AF: 0.0000158 AC: 23AN: 1460222Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726584
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2022 | The c.80T>G (p.M27R) alteration is located in exon 2 (coding exon 2) of the HABP2 gene. This alteration results from a T to G substitution at nucleotide position 80, causing the methionine (M) at amino acid position 27 to be replaced by an arginine (R). 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