chr6-109376082-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM1BP4_StrongBS2
The NM_006016.6(CD164):c.362A>G(p.Asn121Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000866 in 1,570,526 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N121I) has been classified as Uncertain significance.
Frequency
Consequence
NM_006016.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000863 AC: 18AN: 208460Hom.: 0 AF XY: 0.0000700 AC XY: 8AN XY: 114260
GnomAD4 exome AF: 0.0000853 AC: 121AN: 1418322Hom.: 0 Cov.: 28 AF XY: 0.0000879 AC XY: 62AN XY: 705714
GnomAD4 genome AF: 0.0000986 AC: 15AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74360
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 121 of the CD164 protein (p.Asn121Ser). This variant is present in population databases (rs771601649, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with CD164-related conditions. ClinVar contains an entry for this variant (Variation ID: 2174800). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Probably Damaging". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at