6-151548451-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025059.4(CCDC170):c.736G>T(p.Ala246Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,608,846 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025059.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCDC170 | NM_025059.4 | c.736G>T | p.Ala246Ser | missense_variant | 5/11 | ENST00000239374.8 | NP_079335.2 | |
CCDC170 | XM_011536147.3 | c.754G>T | p.Ala252Ser | missense_variant | 5/11 | XP_011534449.1 | ||
CCDC170 | XM_011536148.3 | c.754G>T | p.Ala252Ser | missense_variant | 5/10 | XP_011534450.1 | ||
CCDC170 | XM_047419372.1 | c.736G>T | p.Ala246Ser | missense_variant | 5/10 | XP_047275328.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCDC170 | ENST00000239374.8 | c.736G>T | p.Ala246Ser | missense_variant | 5/11 | 1 | NM_025059.4 | ENSP00000239374.6 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244766Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 133030
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1456722Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 724840
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2022 | The c.736G>T (p.A246S) alteration is located in exon 5 (coding exon 5) of the CCDC170 gene. This alteration results from a G to T substitution at nucleotide position 736, causing the alanine (A) at amino acid position 246 to be replaced by a serine (S). 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