5-102959982-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001177306.2(PAM):c.1013T>A(p.Phe338Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,460,360 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001177306.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250892Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135580
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1460360Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 726550
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2024 | The c.1013T>A (p.F338Y) alteration is located in exon 12 (coding exon 12) of the PAM gene. This alteration results from a T to A substitution at nucleotide position 1013, causing the phenylalanine (F) at amino acid position 338 to be replaced by a tyrosine (Y). 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