chr10-79942421-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003019.5(SFTPD):āc.400A>Gā(p.Lys134Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,046 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003019.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.400A>G | p.Lys134Glu | missense_variant | 4/8 | ENST00000372292.8 | NP_003010.4 | |
SFTPD | XM_011540087.2 | c.400A>G | p.Lys134Glu | missense_variant | 4/8 | XP_011538389.1 | ||
SFTPD | XM_011540088.3 | c.316+342A>G | intron_variant | XP_011538390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.400A>G | p.Lys134Glu | missense_variant | 4/8 | 1 | NM_003019.5 | ENSP00000361366.3 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251192Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135762
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460906Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726584
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.400A>G (p.K134E) alteration is located in exon 4 (coding exon 3) of the SFTPD gene. This alteration results from a A to G substitution at nucleotide position 400, causing the lysine (K) at amino acid position 134 to be replaced by a glutamic acid (E). 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