rs34171309
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_002983.3(CCL3):c.234G>T(p.Glu78Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00595 in 1,613,780 control chromosomes in the GnomAD database, including 311 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in Lovd as Likely benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_002983.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCL3 | NM_002983.3 | c.234G>T | p.Glu78Asp | missense_variant | 3/3 | ENST00000613922.2 | |
CCL3 | NR_168494.1 | n.1007G>T | non_coding_transcript_exon_variant | 2/2 | |||
CCL3 | NR_168495.1 | n.217G>T | non_coding_transcript_exon_variant | 3/3 | |||
CCL3 | NR_168496.1 | n.180G>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCL3 | ENST00000613922.2 | c.234G>T | p.Glu78Asp | missense_variant | 3/3 | 1 | NM_002983.3 | P1 | |
CCL3-AS1 | ENST00000620056.4 | n.390-829C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0243 AC: 3699AN: 152078Hom.: 155 Cov.: 32
GnomAD3 exomes AF: 0.00808 AC: 2030AN: 251206Hom.: 75 AF XY: 0.00651 AC XY: 884AN XY: 135766
GnomAD4 exome AF: 0.00403 AC: 5886AN: 1461584Hom.: 151 Cov.: 31 AF XY: 0.00374 AC XY: 2717AN XY: 727094
GnomAD4 genome ? AF: 0.0244 AC: 3715AN: 152196Hom.: 160 Cov.: 32 AF XY: 0.0246 AC XY: 1831AN XY: 74404
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at