Genetic Variant SFTPD:c.752-19_752-16delGACT (chr10-79938243-AAGTC-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_003019.5(SFTPD):c.752-19_752-16delGACT variant causes a intron change. The variant allele was found at a frequency of 0.0852 in 1,575,720 control chromosomes in the GnomAD database, including 7,328 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.12 ( 1688 hom., cov: 30)

Exomes 𝑓: 0.081 ( 5640 hom. )

Consequence

SFTPD
NM_003019.5 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.61

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 10-79938243-AAGTC-A is Benign according to our data. Variant chr10-79938243-AAGTC-A is described in ClinVar as [Benign]. Clinvar id is 403430.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5 link	c.752-19_752-16delGACT	intron_variant	Intron 7 of 7	ENST00000372292.8	NP_003010.4	P35247
SFTPD	XM_011540087.2 link	c.752-19_752-16delGACT	intron_variant	Intron 7 of 7		XP_011538389.1	P35247
SFTPD	XM_011540088.3 link	c.635-19_635-16delGACT	intron_variant	Intron 6 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8 link	c.752-19_752-16delGACT		intron_variant	Intron 7 of 7	1	NM_003019.5	ENSP00000361366.3		P35247

Frequencies

GnomAD3 genomes

AF:

0.124

AC:

18768

AN:

151938

Hom.:

1688

Cov.:

show subpopulations

Gnomad AFR

AF:

0.245

Gnomad AMI

AF:

0.235

Gnomad AMR

AF:

0.0764

Gnomad ASJ

AF:

0.0283

Gnomad EAS

AF:

0.00174

Gnomad SAS

AF:

0.0207

Gnomad FIN

AF:

0.127

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.0807

Gnomad OTH

AF:

0.108

GnomAD3 exomes

AF:

0.0778

AC:

18138

AN:

233108

Hom.:

1097

AF XY:

0.0737

AC XY:

9277

AN XY:

125846

show subpopulations

Gnomad AFR exome

AF:

0.252

Gnomad AMR exome

AF:

0.0518

Gnomad ASJ exome

AF:

0.0300

Gnomad EAS exome

AF:

0.000606

Gnomad SAS exome

AF:

0.0227

Gnomad FIN exome

AF:

0.133

Gnomad NFE exome

AF:

0.0829

Gnomad OTH exome

AF:

0.0754

GnomAD4 exome

AF:

0.0811

AC:

115456

AN:

1423664

Hom.:

5640

AF XY:

0.0783

AC XY:

54945

AN XY:

702012

show subpopulations

Gnomad4 AFR exome

AF:

0.253

Gnomad4 AMR exome

AF:

0.0543

Gnomad4 ASJ exome

AF:

0.0293

Gnomad4 EAS exome

AF:

0.000743

Gnomad4 SAS exome

AF:

0.0221

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.0835

Gnomad4 OTH exome

AF:

0.0829

GnomAD4 genome

AF:

0.123

AC:

18772

AN:

152056

Hom.:

1688

Cov.:

AF XY:

0.121

AC XY:

9004

AN XY:

74322

show subpopulations

Gnomad4 AFR

AF:

0.244

Gnomad4 AMR

AF:

0.0762

Gnomad4 ASJ

AF:

0.0283

Gnomad4 EAS

AF:

0.00174

Gnomad4 SAS

AF:

0.0205

Gnomad4 FIN

AF:

0.127

Gnomad4 NFE

AF:

0.0807

Gnomad4 OTH

AF:

0.106

Alfa

AF:

0.0938

Hom.:

181

Bravo

AF:

0.128

Asia WGS

AF:

0.0310

AC:

110

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 28, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over