Genetic Variant SFTPD:c.200-87A>G (chr10-79942966-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_003019.5(SFTPD):c.200-87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 838,808 control chromosomes in the GnomAD database, including 14,320 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 0.18 ( 3221 hom., cov: 32)

Exomes 𝑓: 0.15 ( 11099 hom. )

Consequence

SFTPD
NM_003019.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.596

Publications

12 publications found

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]

SFTPD links:

ENSG00000283913 (HGNC:):

ENSG00000283913 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003019.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	NM_003019.5	MANE Select	c.200-87A>G		intron	N/A	NP_003010.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SFTPD	ENST00000372292.8	TSL:1 MANE Select	c.200-87A>G	intron	N/A	ENSP00000361366.3	P35247
SFTPD	ENST00000946714.1		c.368-87A>G	intron	N/A	ENSP00000616773.1
SFTPD	ENST00000946710.1		c.341-87A>G	intron	N/A	ENSP00000616769.1

Frequencies

GnomAD3 genomes

AF:

0.182

AC:

27613

AN:

151948

Hom.:

3208

Cov.:

show subpopulations

Gnomad AFR

AF:

0.286

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.233

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.410

Gnomad SAS

AF:

0.306

Gnomad FIN

AF:

0.0619

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.102

Gnomad OTH

AF:

0.174

GnomAD4 exome

AF:

0.151

AC:

103807

AN:

686742

Hom.:

11099

AF XY:

0.155

AC XY:

56681

AN XY:

366614

show subpopulations

African (AFR)

AF:

0.288

AC:

5215

AN:

18130

American (AMR)

AF:

0.272

AC:

10351

AN:

38122

Ashkenazi Jewish (ASJ)

AF:

0.172

AC:

3259

AN:

18970

East Asian (EAS)

AF:

0.422

AC:

15150

AN:

35876

South Asian (SAS)

AF:

0.276

AC:

18139

AN:

65826

European-Finnish (FIN)

AF:

0.0699

AC:

3329

AN:

47596

Middle Eastern (MID)

AF:

0.164

AC:

591

AN:

3606

European-Non Finnish (NFE)

AF:

0.0997

AC:

42302

AN:

424100

Other (OTH)

AF:

0.159

AC:

5471

AN:

34516

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

4121

8242

12364

16485

20606

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

998

1996

2994

3992

4990

<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:

0.182

AC:

27675

AN:

152066

Hom.:

3221

Cov.:

AF XY:

0.185

AC XY:

13782

AN XY:

74342

show subpopulations

African (AFR)

AF:

0.286

AC:

11859

AN:

41458

American (AMR)

AF:

0.234

AC:

3576

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

600

AN:

3472

East Asian (EAS)

AF:

0.410

AC:

2108

AN:

5142

South Asian (SAS)

AF:

0.306

AC:

1466

AN:

4798

European-Finnish (FIN)

AF:

0.0619

AC:

657

AN:

10612

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.102

AC:

6923

AN:

67980

Other (OTH)

AF:

0.180

AC:

380

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1099

2199

3298

4398

5497

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

294

588

882

1176

1470

<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:

0.0793

Hom.:

134

Bravo

AF:

0.199

Asia WGS

AF:

0.332

AC:

1151

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.9

(source)

DANN

Benign

0.80

PhyloP100

-0.60

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over