Genetic Variant SFTPA1:p.Leu50Ile (chr10-79611973-C-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_005411.5(SFTPA1):c.148C>A(p.Leu50Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L50V) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 29)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

SFTPA1
NM_005411.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.893

Publications

39 publications found

Variant links:

Genes affected

SFTPA1 (HGNC:10798): (surfactant protein A1) This gene encodes a lung surfactant protein that is a member of a subfamily of C-type lectins called collectins. The encoded protein binds specific carbohydrate moieties found on lipids and on the surface of microorganisms. This protein plays an essential role in surfactant homeostasis and in the defense against respiratory pathogens. Mutations in this gene are associated with idiopathic pulmonary fibrosis. Alternate splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

SFTPA1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.060816526).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005411.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SFTPA1	NM_005411.5	MANE Select	c.148C>A	p.Leu50Ile	missense	Exon 3 of 6	NP_005402.3
SFTPA1	NM_001093770.3		c.193C>A	p.Leu65Ile	missense	Exon 3 of 6	NP_001087239.2
SFTPA1	NM_001164644.2		c.148C>A	p.Leu50Ile	missense	Exon 3 of 6	NP_001158116.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
SFTPA1	ENST00000398636.8	TSL:1 MANE Select	c.148C>A	p.Leu50Ile	missense	Exon 3 of 6	ENSP00000381633.3
SFTPA1	ENST00000419470.6	TSL:1	c.193C>A	p.Leu65Ile	missense	Exon 3 of 6	ENSP00000397082.2
SFTPA1	ENST00000428376.6	TSL:1	c.148C>A	p.Leu50Ile	missense	Exon 2 of 5	ENSP00000411102.2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

1436616

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

715414

African (AFR)

AF:

0.00

AC:

AN:

33098

American (AMR)

AF:

0.00

AC:

AN:

44456

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25992

East Asian (EAS)

AF:

0.00

AC:

AN:

39218

South Asian (SAS)

AF:

0.00

AC:

AN:

85802

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53288

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5678

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1089482

Other (OTH)

AF:

0.00

AC:

AN:

59602

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

3611

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.073

BayesDel_addAF

Benign

-0.36

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.12

(source)

DANN

Benign

0.73

DEOGEN2

Benign

0.047

Eigen

Benign

-1.2

Eigen_PC

Benign

-1.2

FATHMM_MKL

Benign

0.0080

LIST_S2

Benign

0.47

M_CAP

Benign

0.00093

MetaRNN

Benign

0.061

MetaSVM

Benign

-0.96

MutationAssessor

Benign

0.14

PhyloP100

-0.89

PrimateAI

Uncertain

0.60

PROVEAN

Benign

0.34

REVEL

Benign

0.046

Sift

Benign

0.55

Sift4G

Benign

0.49

Polyphen

0.0

Vest4

0.10

MutPred

0.20

Gain of methylation at K51 (P = 0.0592)

MVP

0.076

MPC

0.017

ClinPred

0.030

GERP RS

-3.0

Varity_R

0.043

gMVP

0.069

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over