NM_012455.3:c.182A>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_012455.3(PSD4):c.182A>T(p.Gln61Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000546 in 1,613,960 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012455.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000283 AC: 43AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00109 AC: 274AN: 251374Hom.: 3 AF XY: 0.00149 AC XY: 203AN XY: 135866
GnomAD4 exome AF: 0.000573 AC: 838AN: 1461670Hom.: 8 Cov.: 30 AF XY: 0.000814 AC XY: 592AN XY: 727156
GnomAD4 genome AF: 0.000289 AC: 44AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.182A>T (p.Q61L) alteration is located in exon 2 (coding exon 1) of the PSD4 gene. This alteration results from a A to T substitution at nucleotide position 182, causing the glutamine (Q) at amino acid position 61 to be replaced by a leucine (L). 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