chr10-125833906-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_078468.3(BCCIP):c.734C>T(p.Ala245Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000196 in 1,614,026 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A245T) has been classified as Uncertain significance.
Frequency
Consequence
NM_078468.3 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 |
---|---|---|---|---|---|---|---|
BCCIP | NM_078468.3 | c.734C>T | p.Ala245Val | missense_variant | 6/7 | ENST00000278100.11 | |
BCCIP | NM_016567.4 | c.734C>T | p.Ala245Val | missense_variant | 6/8 | ||
BCCIP | NM_078469.3 | c.734C>T | p.Ala245Val | missense_variant | 6/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCCIP | ENST00000278100.11 | c.734C>T | p.Ala245Val | missense_variant | 6/7 | 1 | NM_078468.3 | P1 | |
BCCIP | ENST00000368759.5 | c.734C>T | p.Ala245Val | missense_variant | 6/8 | 1 | |||
BCCIP | ENST00000299130.7 | c.734C>T | p.Ala245Val | missense_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000127 AC: 32AN: 251450Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135904
GnomAD4 exome AF: 0.000207 AC: 303AN: 1461876Hom.: 1 Cov.: 31 AF XY: 0.000190 AC XY: 138AN XY: 727236
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2021 | The c.734C>T (p.A245V) alteration is located in exon 6 (coding exon 6) of the BCCIP gene. This alteration results from a C to T substitution at nucleotide position 734, causing the alanine (A) at amino acid position 245 to be replaced by a valine (V). 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