chr6-26451798-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006994.5(BTN3A3):c.1142G>A(p.Arg381His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000558 in 1,614,050 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_006994.5 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 | UniProt |
---|---|---|---|---|---|---|---|
BTN3A3 | NM_006994.5 | c.1142G>A | p.Arg381His | missense_variant | 11/11 | ENST00000244519.7 | |
BTN3A3 | NM_197974.3 | c.995G>A | p.Arg332His | missense_variant | 10/10 | ||
BTN3A3 | NM_001242803.2 | c.512G>A | p.Arg171His | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BTN3A3 | ENST00000244519.7 | c.1142G>A | p.Arg381His | missense_variant | 11/11 | 1 | NM_006994.5 | P1 | |
ENST00000707189.1 | n.1000-101389G>A | intron_variant, non_coding_transcript_variant | |||||||
ENST00000707191.1 | n.1001-80907G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251484Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135916
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461772Hom.: 0 Cov.: 31 AF XY: 0.0000633 AC XY: 46AN XY: 727180
GnomAD4 genome AF: 0.0000919 AC: 14AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.1142G>A (p.R381H) alteration is located in exon 11 (coding exon 9) of the BTN3A3 gene. This alteration results from a G to A substitution at nucleotide position 1142, causing the arginine (R) at amino acid position 381 to be replaced by a histidine (H). 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