NM_003019.5:c.752-19_752-16delGACT

Variant names:

• chr10-79938243-AAGTC-A
• rs17880072
• NM_003019.5:c.752-19_752-16delGACT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.61
• Publications: 2 publications found

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]

ENSG00000283913 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.752-19_752-16delGACT		intron_variant	Intron 7 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.752-19_752-16delGACT		intron_variant	Intron 7 of 7		XP_011538389.1
SFTPD	XM_011540088.3	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	c.752-19_752-16delGACT		intron_variant	Intron 7 of 7	1	NM_003019.5	ENSP00000361366.3

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18768 AN: 151938 Hom.: 1688 Cov.: 30

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

GnomAD2 exomes AF: 0.0778 AC: 18138 AN: 233108 AF XY: 0.0737

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 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

African (AFR) AF: 0.253 AC: 8318 AN: 32892

American (AMR) AF: 0.0543 AC: 2369 AN: 43600

Ashkenazi Jewish (ASJ) AF: 0.0293 AC: 723 AN: 24698

East Asian (EAS) AF: 0.000743 AC: 29 AN: 39038

South Asian (SAS) AF: 0.0221 AC: 1831 AN: 82972

European-Finnish (FIN) AF: 0.127 AC: 6196 AN: 48620

Middle Eastern (MID) AF: 0.0554 AC: 312 AN: 5630

European-Non Finnish (NFE) AF: 0.0835 AC: 90805 AN: 1087414

Other (OTH) AF: 0.0829 AC: 4873 AN: 58800

GnomAD4 genome AF: 0.123 AC: 18772 AN: 152056 Hom.: 1688 Cov.: 30 AF XY: 0.121 AC XY: 9004 AN XY: 74322

African (AFR) AF: 0.244 AC: 10115 AN: 41432

American (AMR) AF: 0.0762 AC: 1164 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0283 AC: 98 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5172

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1340 AN: 10566

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0807 AC: 5485 AN: 67996

Other (OTH) AF: 0.106 AC: 225 AN: 2116

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

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
PhyloP100		3.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17880072; hg19: chr10-81697999; COSMIC: COSV64852634; COSMIC: COSV64852634;