rs10788338

Positions:

• chr10-79973266-A-C
• chr10-79973266-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-4+8952T>G		intron_variant			XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000444384.3	c.36+9309T>G		intron_variant		3		ENSP00000394325

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

Gnomad4 NFE exome AF: 1.00

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

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.606

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.656

Alfa AF: 0.618 Hom.: 7340

Bravo AF: 0.674

Asia WGS AF: 0.717 AC: 2495 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788338; hg19: chr10-81733022;