10-79946452-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_003019.5(SFTPD):c.199+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00301 in 1,609,382 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003019.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SFTPD | NM_003019.5 | c.199+9G>A | intron_variant | Intron 2 of 7 | ENST00000372292.8 | NP_003010.4 | ||
SFTPD | XM_011540087.2 | c.199+9G>A | intron_variant | Intron 2 of 7 | XP_011538389.1 | |||
SFTPD | XM_011540088.3 | c.199+9G>A | intron_variant | Intron 2 of 6 | XP_011538390.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SFTPD | ENST00000372292.8 | c.199+9G>A | intron_variant | Intron 2 of 7 | 1 | NM_003019.5 | ENSP00000361366.3 | |||
SFTPD | ENST00000444384.3 | c.238+9G>A | intron_variant | Intron 2 of 5 | 3 | ENSP00000394325.1 | ||||
ENSG00000283913 | ENST00000421889.1 | n.334-3576C>T | intron_variant | Intron 3 of 3 | 3 | |||||
ENSG00000283913 | ENST00000453174.7 | n.962-3576C>T | intron_variant | Intron 7 of 7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00219 AC: 334AN: 152230Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00338 AC: 846AN: 250220Hom.: 6 AF XY: 0.00398 AC XY: 539AN XY: 135344
GnomAD4 exome AF: 0.00310 AC: 4510AN: 1457034Hom.: 20 Cov.: 30 AF XY: 0.00335 AC XY: 2426AN XY: 725106
GnomAD4 genome AF: 0.00218 AC: 332AN: 152348Hom.: 1 Cov.: 33 AF XY: 0.00228 AC XY: 170AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:2
199+9G>A in intron 2 of SFTPD: This variant is not expected to have clinical sig nificance because it is not located within the conserved splice consensus sequen ce. It has been identified in 0.4% (32/8600) of European American chromosomes fr om a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washi ngton.edu/EVS; dbSNP rs6413522). -
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not provided Benign:2
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SFTPD-related disorder Benign:1
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