dbSNP rs1914663: SFTPA1:c.173-115C>T (chr10-79612197-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005411.5(SFTPA1):c.173-115C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 1,605,492 control chromosomes in the GnomAD database, including 7,613 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 0.11 ( 1081 hom., cov: 32)

Exomes 𝑓: 0.090 ( 6532 hom. )

Consequence

SFTPA1
NM_005411.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Publications

9 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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPA1	NM_005411.5 link	c.173-115C>T		intron_variant	Intron 3 of 5	ENST00000398636.8	NP_005402.3	Q8IWL2-1A0A024QZP2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
SFTPA1	ENST00000398636.8 link	c.173-115C>T	intron_variant	Intron 3 of 5	1	NM_005411.5	ENSP00000381633.3	Q8IWL2-1
SFTPA1	ENST00000419470.6 link	c.218-115C>T	intron_variant	Intron 3 of 5	1		ENSP00000397082.2	Q8IWL2-2
SFTPA1	ENST00000428376.6 link	c.173-115C>T	intron_variant	Intron 2 of 4	1		ENSP00000411102.2	Q8IWL2-1
SFTPA1	ENST00000429958.5 link	c.173-115C>T	intron_variant	Intron 2 of 4	1		ENSP00000395527.1	A0A0C4DG36

Frequencies

GnomAD3 genomes

AF:

0.111

AC:

16923

AN:

152004

Hom.:

1081

Cov.:

show subpopulations

Gnomad AFR

AF:

0.137

Gnomad AMI

AF:

0.110

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.148

Gnomad EAS

AF:

0.239

Gnomad SAS

AF:

0.0736

Gnomad FIN

AF:

0.0985

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.0877

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.0903

AC:

131242

AN:

1453370

Hom.:

6532

AF XY:

0.0895

AC XY:

64726

AN XY:

723188

show subpopulations

African (AFR)

AF:

0.138

AC:

4597

AN:

33284

American (AMR)

AF:

0.0949

AC:

4234

AN:

44638

Ashkenazi Jewish (ASJ)

AF:

0.143

AC:

3705

AN:

25884

East Asian (EAS)

AF:

0.224

AC:

8882

AN:

39642

South Asian (SAS)

AF:

0.0646

AC:

5491

AN:

85046

European-Finnish (FIN)

AF:

0.108

AC:

5723

AN:

53202

Middle Eastern (MID)

AF:

0.113

AC:

503

AN:

4438

European-Non Finnish (NFE)

AF:

0.0828

AC:

91708

AN:

1107206

Other (OTH)

AF:

0.107

AC:

6399

AN:

60030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

6598

13197

19795

26394

32992

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3446

6892

10338

13784

17230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.111

AC:

16951

AN:

152122

Hom.:

1081

Cov.:

AF XY:

0.113

AC XY:

8410

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.137

AC:

5671

AN:

41488

American (AMR)

AF:

0.114

AC:

1745

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.148

AC:

512

AN:

3468

East Asian (EAS)

AF:

0.240

AC:

1236

AN:

5158

South Asian (SAS)

AF:

0.0738

AC:

356

AN:

4822

European-Finnish (FIN)

AF:

0.0985

AC:

1043

AN:

10590

Middle Eastern (MID)

AF:

0.167

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0877

AC:

5964

AN:

67994

Other (OTH)

AF:

0.131

AC:

275

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

754

1508

2262

3016

3770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

182

364

546

728

910

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0981

Hom.:

Bravo

AF:

0.115

Asia WGS

AF:

0.162

AC:

562

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.13

(source)

DANN

Benign

0.53

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over