2-157443912-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004288.5(CYTIP):c.109G>A(p.Asp37Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000986 in 1,614,156 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004288.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYTIP | NM_004288.5 | c.109G>A | p.Asp37Asn | missense_variant | 1/8 | ENST00000264192.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYTIP | ENST00000264192.8 | c.109G>A | p.Asp37Asn | missense_variant | 1/8 | 1 | NM_004288.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000334 AC: 84AN: 251434Hom.: 0 AF XY: 0.000280 AC XY: 38AN XY: 135894
GnomAD4 exome AF: 0.00105 AC: 1531AN: 1461840Hom.: 2 Cov.: 30 AF XY: 0.00100 AC XY: 729AN XY: 727218
GnomAD4 genome AF: 0.000400 AC: 61AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.109G>A (p.D37N) alteration is located in exon 1 (coding exon 1) of the CYTIP gene. This alteration results from a G to A substitution at nucleotide position 109, causing the aspartic acid (D) at amino acid position 37 to be replaced by an asparagine (N). 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