rs911886

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003019.5(SFTPD):​c.550+130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 721,118 control chromosomes in the GnomAD database, including 3,969 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.058 ( 595 hom., cov: 32)
Exomes 𝑓: 0.062 ( 3374 hom. )

Consequence

SFTPD
NM_003019.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.13
Variant links:
Genes affected
SFTPD (HGNC:10803): (surfactant protein D) The protein encoded by this gene is part of the innate immune response, protecting the lungs against inhaled microorganisms and chemicals. The encoded protein may also be involved in surfactant metabolism. [provided by RefSeq, Jul 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SFTPDNM_003019.5 linkuse as main transcriptc.550+130G>A intron_variant ENST00000372292.8
SFTPDXM_011540087.2 linkuse as main transcriptc.550+130G>A intron_variant
SFTPDXM_011540088.3 linkuse as main transcriptc.433+130G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SFTPDENST00000372292.8 linkuse as main transcriptc.550+130G>A intron_variant 1 NM_003019.5 P1

Frequencies

GnomAD3 genomes
AF:
0.0581
AC:
8835
AN:
152112
Hom.:
597
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0696
Gnomad AMI
AF:
0.0450
Gnomad AMR
AF:
0.0406
Gnomad ASJ
AF:
0.0539
Gnomad EAS
AF:
0.390
Gnomad SAS
AF:
0.107
Gnomad FIN
AF:
0.0138
Gnomad MID
AF:
0.0918
Gnomad NFE
AF:
0.0336
Gnomad OTH
AF:
0.0531
GnomAD4 exome
AF:
0.0621
AC:
35321
AN:
568888
Hom.:
3374
AF XY:
0.0635
AC XY:
19353
AN XY:
304776
show subpopulations
Gnomad4 AFR exome
AF:
0.0678
Gnomad4 AMR exome
AF:
0.0262
Gnomad4 ASJ exome
AF:
0.0521
Gnomad4 EAS exome
AF:
0.390
Gnomad4 SAS exome
AF:
0.0940
Gnomad4 FIN exome
AF:
0.0149
Gnomad4 NFE exome
AF:
0.0322
Gnomad4 OTH exome
AF:
0.0596
GnomAD4 genome
AF:
0.0581
AC:
8840
AN:
152230
Hom.:
595
Cov.:
32
AF XY:
0.0606
AC XY:
4510
AN XY:
74432
show subpopulations
Gnomad4 AFR
AF:
0.0695
Gnomad4 AMR
AF:
0.0405
Gnomad4 ASJ
AF:
0.0539
Gnomad4 EAS
AF:
0.389
Gnomad4 SAS
AF:
0.108
Gnomad4 FIN
AF:
0.0138
Gnomad4 NFE
AF:
0.0337
Gnomad4 OTH
AF:
0.0558
Alfa
AF:
0.0412
Hom.:
25
Bravo
AF:
0.0618
Asia WGS
AF:
0.184
AC:
638
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.14
DANN
Benign
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs911886; hg19: chr10-81701580; COSMIC: COSV64852587; API