17-76685082-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_198530.4(MXRA7):c.490G>A(p.Glu164Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,613,976 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_198530.4 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: 0.0000329 AC: 5AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251404Hom.: 2 AF XY: 0.0000589 AC XY: 8AN XY: 135878
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461744Hom.: 3 Cov.: 31 AF XY: 0.0000303 AC XY: 22AN XY: 727194
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74428
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.490G>A (p.E164K) alteration is located in exon 3 (coding exon 3) of the MXRA7 gene. This alteration results from a G to A substitution at nucleotide position 490, causing the glutamic acid (E) at amino acid position 164 to be replaced by a lysine (K). 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