chr4-101870640-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017935.5(BANK1):c.899G>T(p.Cys300Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,609,310 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017935.5 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 |
---|---|---|---|---|---|---|---|
BANK1 | NM_017935.5 | c.899G>T | p.Cys300Phe | missense_variant | 5/17 | ENST00000322953.9 | |
BANK1 | NM_001083907.3 | c.809G>T | p.Cys270Phe | missense_variant | 5/17 | ||
BANK1 | NM_001127507.3 | c.500G>T | p.Cys167Phe | missense_variant | 4/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BANK1 | ENST00000322953.9 | c.899G>T | p.Cys300Phe | missense_variant | 5/17 | 1 | NM_017935.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000789 AC: 120AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000158 AC: 39AN: 246918Hom.: 0 AF XY: 0.0000898 AC XY: 12AN XY: 133582
GnomAD4 exome AF: 0.0000741 AC: 108AN: 1457190Hom.: 0 Cov.: 31 AF XY: 0.0000635 AC XY: 46AN XY: 724888
GnomAD4 genome ? AF: 0.000782 AC: 119AN: 152120Hom.: 0 Cov.: 32 AF XY: 0.000793 AC XY: 59AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 14, 2023 | The c.899G>T (p.C300F) alteration is located in exon 5 (coding exon 5) of the BANK1 gene. This alteration results from a G to T substitution at nucleotide position 899, causing the cysteine (C) at amino acid position 300 to be replaced by a phenylalanine (F). 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