5-149301147-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152406.4(AFAP1L1):c.244G>A(p.Asp82Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000366 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152406.4 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: 0.000250 AC: 38AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000477 AC: 12AN: 251394Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135860
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461666Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727126
GnomAD4 genome AF: 0.000250 AC: 38AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000215 AC XY: 16AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.244G>A (p.D82N) alteration is located in exon 4 (coding exon 4) of the AFAP1L1 gene. This alteration results from a G to A substitution at nucleotide position 244, causing the aspartic acid (D) at amino acid position 82 to be replaced by an asparagine (N). 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