Genetic Variant SFTPD:c.36+9309T>G (chr10-79973266-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000444384.3(SFTPD):c.36+9309T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 151,908 control chromosomes in the GnomAD database, including 34,697 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 0.67 ( 34696 hom., cov: 31)

Exomes 𝑓: 1.0 ( 1 hom. )

Consequence

SFTPD
ENST00000444384.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.41

Publications

7 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:

SFTPD-AS1 (HGNC:51589): (SFTPD antisense RNA 1)

SFTPD-AS1 links:

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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=-1.06).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2 link	c.-4+8952T>G		intron_variant	Intron 1 of 7		XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000444384.3 link	c.36+9309T>G		intron_variant	Intron 1 of 5	3		ENSP00000394325.1
SFTPD-AS1	ENST00000608229.1 link	n.*53A>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

101014

AN:

151788

Hom.:

34636

Cov.:

show subpopulations

Gnomad AFR

AF:

0.844

Gnomad AMI

AF:

0.625

Gnomad AMR

AF:

0.618

Gnomad ASJ

AF:

0.606

Gnomad EAS

AF:

0.620

Gnomad SAS

AF:

0.742

Gnomad FIN

AF:

0.549

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.588

Gnomad OTH

AF:

0.651

GnomAD4 exome

AF:

1.00

AC:

AN:

Hom.:

AF XY:

1.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.666

AC:

101135

AN:

151906

Hom.:

34696

Cov.:

AF XY:

0.665

AC XY:

49362

AN XY:

74218

show subpopulations

African (AFR)

AF:

0.844

AC:

34979

AN:

41454

American (AMR)

AF:

0.618

AC:

9431

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.606

AC:

2102

AN:

3466

East Asian (EAS)

AF:

0.620

AC:

3197

AN:

5158

South Asian (SAS)

AF:

0.742

AC:

3570

AN:

4810

European-Finnish (FIN)

AF:

0.549

AC:

5765

AN:

10500

Middle Eastern (MID)

AF:

0.701

AC:

206

AN:

294

European-Non Finnish (NFE)

AF:

0.588

AC:

39931

AN:

67944

Other (OTH)

AF:

0.656

AC:

1384

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1622

3243

4865

6486

8108

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.622

Hom.:

7617

Bravo

AF:

0.674

Asia WGS

AF:

0.717

AC:

2495

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.1

CADD

Benign

0.19

(source)

DANN

Benign

0.46

PhyloP100

-3.4

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over