ENST00000444384.3:c.36+9309T>G

Variant names:

• chr10-79973266-A-C
• rs10788338
• ENST00000444384.3:c.36+9309T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.41
• Publications: 7 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]

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

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444384.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	ENST00000444384.3	TSL:3	c.36+9309T>G		intron	N/A	ENSP00000394325.1
	SFTPD-AS1	ENST00000608229.1	TSL:6	n.*53A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101014 AN: 151788 Hom.: 34636 Cov.: 31

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: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 2 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.666 AC: 101135 AN: 151906 Hom.: 34696 Cov.: 31 AF XY: 0.665 AC XY: 49362 AN XY: 74218

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.46
PhyloP100		-3.4
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10788338; hg19: chr10-81733022;