chr6-26370570-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_007047.5(BTN3A2):c.682G>A(p.Gly228Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000112 in 1,614,158 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 Likely benign (★).
Frequency
Consequence
NM_007047.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BTN3A2 | NM_007047.5 | c.682G>A | p.Gly228Ser | missense_variant | 5/11 | ENST00000377708.7 | NP_008978.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BTN3A2 | ENST00000377708.7 | c.682G>A | p.Gly228Ser | missense_variant | 5/11 | 1 | NM_007047.5 | ENSP00000366937 | P2 | |
ENST00000707189.1 | n.1000-182617G>A | intron_variant, non_coding_transcript_variant | ||||||||
ENST00000707191.1 | n.1001-162135G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000854 AC: 13AN: 152160Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251312Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135844
GnomAD4 exome AF: 0.000114 AC: 167AN: 1461880Hom.: 0 Cov.: 34 AF XY: 0.000109 AC XY: 79AN XY: 727240
GnomAD4 genome AF: 0.0000854 AC: 13AN: 152278Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at