3-108355373-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001282556.2(HHLA2):c.677C>T(p.Thr226Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000695 in 1,612,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001282556.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000811 AC: 20AN: 246480Hom.: 0 AF XY: 0.0000598 AC XY: 8AN XY: 133868
GnomAD4 exome AF: 0.0000596 AC: 87AN: 1460230Hom.: 0 Cov.: 32 AF XY: 0.0000427 AC XY: 31AN XY: 726246
GnomAD4 genome AF: 0.000164 AC: 25AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74418
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.677C>T (p.T226M) alteration is located in exon 5 (coding exon 3) of the HHLA2 gene. This alteration results from a C to T substitution at nucleotide position 677, causing the threonine (T) at amino acid position 226 to be replaced by a methionine (M). 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