X-110171452-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032227.4(TMEM164):c.619C>T(p.Arg207Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000091 in 1,208,152 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 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. R207L) has been classified as Uncertain significance.
Frequency
Consequence
NM_032227.4 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: 0.00000896 AC: 1AN: 111651Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33821
GnomAD3 exomes AF: 0.0000221 AC: 4AN: 181187Hom.: 0 AF XY: 0.0000304 AC XY: 2AN XY: 65689
GnomAD4 exome AF: 0.00000912 AC: 10AN: 1096501Hom.: 0 Cov.: 29 AF XY: 0.0000111 AC XY: 4AN XY: 361905
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111651Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33821
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.619C>T (p.R207W) alteration is located in exon 6 (coding exon 5) of the TMEM164 gene. This alteration results from a C to T substitution at nucleotide position 619, causing the arginine (R) at amino acid position 207 to be replaced by a tryptophan (W). 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