2-168923754-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003742.4(ABCB11):c.3834C>T(p.Ser1278=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,722 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. S1278S) has been classified as Uncertain significance.
Frequency
Consequence
NM_003742.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCB11 | NM_003742.4 | c.3834C>T | p.Ser1278= | synonymous_variant | 28/28 | ENST00000650372.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCB11 | ENST00000650372.1 | c.3834C>T | p.Ser1278= | synonymous_variant | 28/28 | NM_003742.4 | P1 | ||
ABCB11 | ENST00000649448.1 | c.2211C>T | p.Ser737= | synonymous_variant | 15/15 | ||||
ABCB11 | ENST00000648875.1 | c.226+903C>T | intron_variant | ||||||
ABCB11 | ENST00000439188.1 | c.*2232C>T | 3_prime_UTR_variant, NMD_transcript_variant | 15/15 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247278Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134364
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461722Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727146
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at