rs1923534

Positions:

• chr10-79950729-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000444384.3(SFTPD):​c.37-4067T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0694 in 152,306 control chromosomes in the GnomAD database, including 571 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 0.069 (571 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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=-0.75).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPD	XM_011540087.2	c.-3-4067T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPD	ENST00000444384.3	c.37-4067T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10548 AN: 152188 Hom.: 564 Cov.: 32

Gnomad AFR AF: 0.0299

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0860

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.0694 AC: 10577 AN: 152306 Hom.: 571 Cov.: 32 AF XY: 0.0731 AC XY: 5441 AN XY: 74470

Gnomad4 AFR AF: 0.0300

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0784

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.0484

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.0898

Alfa AF: 0.0668 Hom.: 66

Bravo AF: 0.0752

Asia WGS AF: 0.126 AC: 438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	13
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923534; hg19: chr10-81710485;