10-79557289-G-T
Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBA1
The NM_001098668.4(SFTPA2):c.667C>A(p.Gln223Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 1,613,734 control chromosomes in the GnomAD database, including 38,163 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001098668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -18 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPA2 | ENST00000372325.7 | c.667C>A | p.Gln223Lys | missense_variant | Exon 6 of 6 | 1 | NM_001098668.4 | ENSP00000361400.2 | ||
SFTPA2 | ENST00000372327.9 | c.667C>A | p.Gln223Lys | missense_variant | Exon 5 of 5 | 1 | ENSP00000361402.5 |
Frequencies
GnomAD3 genomes AF: 0.250 AC: 37959AN: 151766Hom.: 5265 Cov.: 32
GnomAD3 exomes AF: 0.217 AC: 54596AN: 251408Hom.: 6547 AF XY: 0.223 AC XY: 30291AN XY: 135878
GnomAD4 exome AF: 0.207 AC: 301937AN: 1461850Hom.: 32886 Cov.: 34 AF XY: 0.210 AC XY: 152941AN XY: 727230
GnomAD4 genome AF: 0.250 AC: 38017AN: 151884Hom.: 5277 Cov.: 32 AF XY: 0.249 AC XY: 18518AN XY: 74222
ClinVar
Submissions by phenotype
not provided Benign:2
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This variant is associated with the following publications: (PMID: 26436397, 24950659, 16292672, 23056344, 20466729) -
not specified Benign:1
p.Gln223Lys in exon 6 of SFTPA2: This variant is not expected to have clinical s ignificance because it has been identified in 36% (1576/4406) of African America n chromosomes by the NHLBI Exome Sequencing Project (http://evs.gs.washington.ed u/EVS/; dbSNP rs1965708). -
Interstitial lung disease 2 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at