chr3-39333266-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005201.4(CCR8):c.935C>T(p.Ser312Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★).
Frequency
Consequence
NM_005201.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCR8 | ENST00000326306.5 | c.935C>T | p.Ser312Leu | missense_variant | Exon 2 of 2 | 1 | NM_005201.4 | ENSP00000326432.4 | ||
CCR8 | ENST00000414803.1 | c.*405C>T | 3_prime_UTR_variant | Exon 3 of 3 | 1 | ENSP00000390104.1 | ||||
ENSG00000287780 | ENST00000655387.1 | n.370-40316G>A | intron_variant | Intron 3 of 3 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250320Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135338
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461816Hom.: 0 Cov.: 33 AF XY: 0.00000688 AC XY: 5AN XY: 727212
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.935C>T (p.S312L) alteration is located in exon 2 (coding exon 1) of the CCR8 gene. This alteration results from a C to T substitution at nucleotide position 935, causing the serine (S) at amino acid position 312 to be replaced by a leucine (L). 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