2-171554763-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The ENST00000321348.9(CYBRD1):c.797G>A(p.Ser266Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 1,613,702 control chromosomes in the GnomAD database, including 361,957 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
ENST00000321348.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CYBRD1 | NM_024843.4 | c.797G>A | p.Ser266Asn | missense_variant | 4/4 | ENST00000321348.9 | NP_079119.3 | |
CYBRD1 | NM_001256909.2 | c.623G>A | p.Ser208Asn | missense_variant | 4/4 | NP_001243838.1 | ||
CYBRD1 | NM_001127383.2 | c.*114G>A | 3_prime_UTR_variant | 3/3 | NP_001120855.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CYBRD1 | ENST00000321348.9 | c.797G>A | p.Ser266Asn | missense_variant | 4/4 | 1 | NM_024843.4 | ENSP00000319141 | P1 | |
CYBRD1 | ENST00000375252.3 | c.*114G>A | 3_prime_UTR_variant | 3/3 | 1 | ENSP00000364401 | ||||
CYBRD1 | ENST00000409484.5 | c.623G>A | p.Ser208Asn | missense_variant | 4/4 | 2 | ENSP00000386739 |
Frequencies
GnomAD3 genomes AF: 0.709 AC: 107792AN: 151952Hom.: 39385 Cov.: 32
GnomAD3 exomes AF: 0.641 AC: 160756AN: 250712Hom.: 53120 AF XY: 0.641 AC XY: 86828AN XY: 135494
GnomAD4 exome AF: 0.661 AC: 965561AN: 1461628Hom.: 322528 Cov.: 61 AF XY: 0.659 AC XY: 479435AN XY: 727126
GnomAD4 genome AF: 0.710 AC: 107897AN: 152074Hom.: 39429 Cov.: 32 AF XY: 0.706 AC XY: 52437AN XY: 74324
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at