8-132079763-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145095.3(HHLA1):c.880G>T(p.Ala294Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000709 in 1,551,376 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145095.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HHLA1 | NM_001145095.3 | c.880G>T | p.Ala294Ser | missense_variant | 11/17 | ENST00000414222.2 | NP_001138567.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HHLA1 | ENST00000414222.2 | c.880G>T | p.Ala294Ser | missense_variant | 11/17 | 5 | NM_001145095.3 | ENSP00000388322.1 | ||
ENSG00000258417 | ENST00000262283.5 | c.152-1792G>T | intron_variant | 5 | ENSP00000262283.5 | |||||
HHLA1 | ENST00000473291.1 | n.1342G>T | non_coding_transcript_exon_variant | 1/7 | 1 | |||||
HHLA1 | ENST00000673615.1 | c.988G>T | p.Ala330Ser | missense_variant | 12/18 | ENSP00000500443.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152200Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000500 AC: 7AN: 1399176Hom.: 0 Cov.: 32 AF XY: 0.00000580 AC XY: 4AN XY: 690098
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.880G>T (p.A294S) alteration is located in exon 10 (coding exon 10) of the HHLA1 gene. This alteration results from a G to T substitution at nucleotide position 880, causing the alanine (A) at amino acid position 294 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