2-96828648-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017623.5(CNNM3):c.1868C>T(p.Ala623Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000867 in 1,614,158 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017623.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000421 AC: 64AN: 152154Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000131 AC: 33AN: 251248Hom.: 0 AF XY: 0.000103 AC XY: 14AN XY: 135806
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461886Hom.: 0 Cov.: 31 AF XY: 0.0000481 AC XY: 35AN XY: 727244
GnomAD4 genome AF: 0.000420 AC: 64AN: 152272Hom.: 1 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1868C>T (p.A623V) alteration is located in exon 6 (coding exon 6) of the CNNM3 gene. This alteration results from a C to T substitution at nucleotide position 1868, causing the alanine (A) at amino acid position 623 to be replaced by a valine (V). 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