chr21-29326764-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001186.4(BACH1):c.940T>C(p.Ser314Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00413 in 1,614,012 control chromosomes in the GnomAD database, including 238 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001186.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BACH1 | NM_001186.4 | c.940T>C | p.Ser314Pro | missense_variant | 3/5 | ENST00000286800.8 | |
BACH1 | NM_206866.3 | c.940T>C | p.Ser314Pro | missense_variant | 3/5 | ||
BACH1 | NR_027655.3 | n.1119T>C | non_coding_transcript_exon_variant | 3/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BACH1 | ENST00000286800.8 | c.940T>C | p.Ser314Pro | missense_variant | 3/5 | 1 | NM_001186.4 | P1 | |
BACH1 | ENST00000399921.5 | c.940T>C | p.Ser314Pro | missense_variant | 3/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0227 AC: 3452AN: 152192Hom.: 111 Cov.: 33
GnomAD3 exomes AF: 0.00572 AC: 1434AN: 250848Hom.: 55 AF XY: 0.00427 AC XY: 580AN XY: 135752
GnomAD4 exome AF: 0.00220 AC: 3209AN: 1461702Hom.: 126 Cov.: 31 AF XY: 0.00190 AC XY: 1383AN XY: 727154
GnomAD4 genome ? AF: 0.0227 AC: 3457AN: 152310Hom.: 112 Cov.: 33 AF XY: 0.0218 AC XY: 1622AN XY: 74476
ClinVar
Submissions by phenotype
BACH1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at