Genetic Variant NM_003019.5:c.297G>A (chr10-79942782-C-T) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_003019.5(SFTPD):c.297G>A(p.Lys99Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0186 in 1,612,094 control chromosomes in the GnomAD database, including 454 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.033 ( 136 hom., cov: 32)

Exomes 𝑓: 0.017 ( 318 hom. )

Consequence

SFTPD
NM_003019.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.138

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.32).

BP6

Variant 10-79942782-C-T is Benign according to our data. Variant chr10-79942782-C-T is described in ClinVar as [Benign]. Clinvar id is 165217.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-79942782-C-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.138 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.074 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5 link	c.297G>A	p.Lys99Lys	synonymous_variant	Exon 3 of 8	ENST00000372292.8	NP_003010.4	P35247
SFTPD	XM_011540087.2 link	c.297G>A	p.Lys99Lys	synonymous_variant	Exon 3 of 8		XP_011538389.1	P35247
SFTPD	XM_011540088.3 link	c.297G>A	p.Lys99Lys	synonymous_variant	Exon 3 of 7		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8 link	c.297G>A	p.Lys99Lys	synonymous_variant	Exon 3 of 8	1	NM_003019.5	ENSP00000361366.3		P35247

Frequencies

GnomAD3 genomes

AF:

0.0329

AC:

5006

AN:

152140

Hom.:

133

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0759

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0289

Gnomad ASJ

AF:

0.0190

Gnomad EAS

AF:

0.000387

Gnomad SAS

AF:

0.00600

Gnomad FIN

AF:

0.00226

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0175

Gnomad OTH

AF:

0.0421

GnomAD3 exomes

AF:

0.0176

AC:

4436

AN:

251436

Hom.:

AF XY:

0.0171

AC XY:

2326

AN XY:

135884

show subpopulations

Gnomad AFR exome

AF:

0.0720

Gnomad AMR exome

AF:

0.0176

Gnomad ASJ exome

AF:

0.0195

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00728

Gnomad FIN exome

AF:

0.00245

Gnomad NFE exome

AF:

0.0180

Gnomad OTH exome

AF:

0.0217

GnomAD4 exome

AF:

0.0171

AC:

25025

AN:

1459836

Hom.:

318

Cov.:

AF XY:

0.0169

AC XY:

12264

AN XY:

726366

show subpopulations

Gnomad4 AFR exome

AF:

0.0767

Gnomad4 AMR exome

AF:

0.0179

Gnomad4 ASJ exome

AF:

0.0193

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00807

Gnomad4 FIN exome

AF:

0.00296

Gnomad4 NFE exome

AF:

0.0168

Gnomad4 OTH exome

AF:

0.0229

GnomAD4 genome

AF:

0.0330

AC:

5024

AN:

152258

Hom.:

136

Cov.:

AF XY:

0.0322

AC XY:

2399

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0762

Gnomad4 AMR

AF:

0.0289

Gnomad4 ASJ

AF:

0.0190

Gnomad4 EAS

AF:

0.000388

Gnomad4 SAS

AF:

0.00601

Gnomad4 FIN

AF:

0.00226

Gnomad4 NFE

AF:

0.0175

Gnomad4 OTH

AF:

0.0417

Alfa

AF:

0.0233

Hom.:

Bravo

AF:

0.0359

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0221

EpiControl

AF:

0.0251

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Feb 21, 2013

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Lys99Lys in exon 3 of SFTPD: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 7.5% (331/4406) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs17885228). -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.32

CADD

Benign

6.5

DANN

Benign

0.67

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