X-3310339-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_015419.4(MXRA5):c.7864G>A(p.Ala2622Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000117 in 1,199,384 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. A2622A) has been classified as Benign.
Frequency
Consequence
NM_015419.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000183 AC: 2AN: 109562Hom.: 0 Cov.: 21 AF XY: 0.0000628 AC XY: 2AN XY: 31822
GnomAD3 exomes AF: 0.0000111 AC: 2AN: 180209Hom.: 0 AF XY: 0.0000152 AC XY: 1AN XY: 65787
GnomAD4 exome AF: 0.0000110 AC: 12AN: 1089822Hom.: 0 Cov.: 31 AF XY: 0.00000562 AC XY: 2AN XY: 355590
GnomAD4 genome AF: 0.0000183 AC: 2AN: 109562Hom.: 0 Cov.: 21 AF XY: 0.0000628 AC XY: 2AN XY: 31822
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.7864G>A (p.A2622T) alteration is located in exon 7 (coding exon 6) of the MXRA5 gene. This alteration results from a G to A substitution at nucleotide position 7864, causing the alanine (A) at amino acid position 2622 to be replaced by a threonine (T). 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