rs1650232
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 4P and 9B. PVS1_StrongBP6BS1BS2
The NM_001320813.2(SFTPA2):c.-26-2G>T variant causes a splice acceptor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00259 in 1,585,742 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001320813.2 splice_acceptor, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0116 AC: 1751AN: 151246Hom.: 34 Cov.: 28
GnomAD3 exomes AF: 0.00363 AC: 719AN: 198208Hom.: 21 AF XY: 0.00275 AC XY: 294AN XY: 106726
GnomAD4 exome AF: 0.00163 AC: 2341AN: 1434376Hom.: 27 Cov.: 55 AF XY: 0.00147 AC XY: 1046AN XY: 713470
GnomAD4 genome AF: 0.0116 AC: 1759AN: 151366Hom.: 34 Cov.: 28 AF XY: 0.0110 AC XY: 809AN XY: 73874
ClinVar
Submissions by phenotype
SFTPA2-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 07, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at