9-34709419-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_002989.4(CCL21):c.380G>A(p.Arg127Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000249 in 1,610,192 control chromosomes in the GnomAD database, including 2 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_002989.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCL21 | NM_002989.4 | c.380G>A | p.Arg127Gln | missense_variant | 4/4 | ENST00000259607.7 | NP_002980.1 | |
PHF24 | XM_047423102.1 | c.133+6381C>T | intron_variant | XP_047279058.1 | ||||
PHF24 | XM_047423103.1 | c.70+6381C>T | intron_variant | XP_047279059.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCL21 | ENST00000259607.7 | c.380G>A | p.Arg127Gln | missense_variant | 4/4 | 1 | NM_002989.4 | ENSP00000259607.2 | ||
CCL21 | ENST00000378792 | c.*77G>A | 3_prime_UTR_variant | 3/3 | 2 | ENSP00000368069.1 | ||||
ENSG00000288583 | ENST00000664167.1 | n.86+6381C>T | intron_variant |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000405 AC: 100AN: 247110Hom.: 0 AF XY: 0.000374 AC XY: 50AN XY: 133824
GnomAD4 exome AF: 0.000255 AC: 372AN: 1457920Hom.: 2 Cov.: 31 AF XY: 0.000244 AC XY: 177AN XY: 725464
GnomAD4 genome AF: 0.000190 AC: 29AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74452
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at