chr17-40555370-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001838.4(CCR7):c.509G>A(p.Arg170His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,613,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001838.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CCR7 | ENST00000246657.2 | c.509G>A | p.Arg170His | missense_variant | Exon 3 of 3 | 1 | NM_001838.4 | ENSP00000246657.2 | ||
CCR7 | ENST00000579344.1 | c.491G>A | p.Arg164His | missense_variant | Exon 3 of 3 | 1 | ENSP00000462631.1 | |||
CCR7 | ENST00000578085.1 | c.320G>A | p.Arg107His | missense_variant | Exon 2 of 2 | 3 | ENSP00000463075.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000478 AC: 12AN: 251232Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135782
GnomAD4 exome AF: 0.000265 AC: 388AN: 1461824Hom.: 0 Cov.: 32 AF XY: 0.000263 AC XY: 191AN XY: 727210
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.509G>A (p.R170H) alteration is located in exon 3 (coding exon 3) of the CCR7 gene. This alteration results from a G to A substitution at nucleotide position 509, causing the arginine (R) at amino acid position 170 to be replaced by a histidine (H). 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