Genetic Variant NM_003019.5:c.752-113C>T (chr10-79938341-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003019.5(SFTPD):c.752-113C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 882,676 control chromosomes in the GnomAD database, including 176,824 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.68 ( 35667 hom., cov: 31)

Exomes 𝑓: 0.62 ( 141157 hom. )

Consequence

SFTPD
NM_003019.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.85

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 10-79938341-G-A is Benign according to our data. Variant chr10-79938341-G-A is described in ClinVar as [Benign]. Clinvar id is 1239741.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5 link	c.752-113C>T	intron_variant	Intron 7 of 7	ENST00000372292.8	NP_003010.4	P35247
SFTPD	XM_011540087.2 link	c.752-113C>T	intron_variant	Intron 7 of 7		XP_011538389.1	P35247
SFTPD	XM_011540088.3 link	c.635-113C>T	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.752-113C>T		intron_variant	Intron 7 of 7	1	NM_003019.5	ENSP00000361366.3		P35247

Frequencies

GnomAD3 genomes

AF:

0.677

AC:

102766

AN:

151826

Hom.:

35609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.825

Gnomad AMI

AF:

0.623

Gnomad AMR

AF:

0.647

Gnomad ASJ

AF:

0.639

Gnomad EAS

AF:

0.779

Gnomad SAS

AF:

0.734

Gnomad FIN

AF:

0.592

Gnomad MID

AF:

0.697

Gnomad NFE

AF:

0.598

Gnomad OTH

AF:

0.666

GnomAD4 exome

AF:

0.618

AC:

451638

AN:

730732

Hom.:

141157

AF XY:

0.621

AC XY:

232819

AN XY:

374790

show subpopulations

Gnomad4 AFR exome

AF:

0.827

Gnomad4 AMR exome

AF:

0.611

Gnomad4 ASJ exome

AF:

0.635

Gnomad4 EAS exome

AF:

0.740

Gnomad4 SAS exome

AF:

0.718

Gnomad4 FIN exome

AF:

0.606

Gnomad4 NFE exome

AF:

0.590

Gnomad4 OTH exome

AF:

0.639

GnomAD4 genome

AF:

0.677

AC:

102889

AN:

151944

Hom.:

35667

Cov.:

AF XY:

0.679

AC XY:

50412

AN XY:

74260

show subpopulations

Gnomad4 AFR

AF:

0.825

Gnomad4 AMR

AF:

0.648

Gnomad4 ASJ

AF:

0.639

Gnomad4 EAS

AF:

0.779

Gnomad4 SAS

AF:

0.734

Gnomad4 FIN

AF:

0.592

Gnomad4 NFE

AF:

0.598

Gnomad4 OTH

AF:

0.671

Alfa

AF:

0.652

Hom.:

4376

Bravo

AF:

0.685

Asia WGS

AF:

0.772

AC:

2685

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.18

DANN

Benign

0.52

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