rs727503418

Positions:

• chr2-85663779-C-A
• chr2-85663779-C-G
• chr2-85663779-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000542.5(SFTPB):​c.741G>T​(p.Gln247His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. Q247Q) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SFTPB NM_000542.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

Genes affected

SFTPB (HGNC:10801): (surfactant protein B) This gene encodes the pulmonary-associated surfactant protein B (SPB), an amphipathic surfactant protein essential for lung function and homeostasis after birth. Pulmonary surfactant is a surface-active lipoprotein complex composed of 90% lipids and 10% proteins which include plasma proteins and apolipoproteins SPA, SPB, SPC and SPD. The surfactant is secreted by the alveolar cells of the lung and maintains the stability of pulmonary tissue by reducing the surface tension of fluids that coat the lung. The SPB enhances the rate of spreading and increases the stability of surfactant monolayers in vitro. Multiple mutations in this gene have been identified, which cause pulmonary surfactant metabolism dysfunction type 1, also called pulmonary alveolar proteinosis due to surfactant protein B deficiency, and are associated with fatal respiratory distress in the neonatal period. Alternatively spliced transcript variants encoding the same protein have been identified.[provided by RefSeq, Feb 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPB	NM_000542.5	c.741G>T	p.Gln247His	missense_variant	7/11	ENST00000519937.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPB	ENST00000519937.7	c.741G>T	p.Gln247His	missense_variant	7/11	1	NM_000542.5	P1
SFTPB	ENST00000393822.7	c.741G>T	p.Gln247His	missense_variant	8/12	1		P1
SFTPB	ENST00000409383.6	c.741G>T	p.Gln247His	missense_variant	8/12	1		P1
SFTPB	ENST00000428225.5	c.732G>T	p.Gln244His	missense_variant	7/11	2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Uncertain	0.082	D
BayesDel_noAF	Benign	-0.12
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.68	D;D;T
Eigen	Benign	0.064
Eigen_PC	Benign	0.13
FATHMM_MKL	Benign	0.60	D
LIST_S2	Benign	0.67	.;T;T
M_CAP	Benign	0.032	D
MetaRNN	Uncertain	0.67	D;D;D
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	0.75	N;N;.
MutationTaster	Benign	0.56	N;N;N
PrimateAI	Benign	0.48	T
PROVEAN	Uncertain	-2.6	.;.;D
REVEL	Uncertain	0.54
Sift	Benign	0.091	.;.;T
Sift4G	Benign	0.19	T;T;T
Polyphen		0.82	P;P;P
Vest4		0.65
MutPred		0.64		.;.;Loss of helix (P = 0.2271);
MVP		0.89
MPC		0.60
ClinPred		0.93	D
GERP RS		3.4
Varity_R		0.20
gMVP		0.60

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-85890902;