10-79941824-C-T

Position:

• chr10-79941824-C-T

Variant summary

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

The NM_003019.5(SFTPD):​c.550+130G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0612 in 721,118 control chromosomes in the GnomAD database, including 3,969 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 0.058 (595 hom., cov: 32)
  • Exomes 𝑓: 0.062 (3374 hom.)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPD	NM_003019.5	c.550+130G>A		intron_variant		ENST00000372292.8
SFTPD	XM_011540087.2	c.550+130G>A		intron_variant
SFTPD	XM_011540088.3	c.433+130G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPD	ENST00000372292.8	c.550+130G>A		intron_variant		1	NM_003019.5	P1

Frequencies

GnomAD3 genomes AF: 0.0581 AC: 8835 AN: 152112 Hom.: 597 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0406

Gnomad ASJ AF: 0.0539

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0336

Gnomad OTH AF: 0.0531

GnomAD4 exome AF: 0.0621 AC: 35321 AN: 568888 Hom.: 3374 AF XY: 0.0635 AC XY: 19353 AN XY: 304776

Gnomad4 AFR exome AF: 0.0678

Gnomad4 AMR exome AF: 0.0262

Gnomad4 ASJ exome AF: 0.0521

Gnomad4 EAS exome AF: 0.390

Gnomad4 SAS exome AF: 0.0940

Gnomad4 FIN exome AF: 0.0149

Gnomad4 NFE exome AF: 0.0322

Gnomad4 OTH exome AF: 0.0596

GnomAD4 genome AF: 0.0581 AC: 8840 AN: 152230 Hom.: 595 Cov.: 32 AF XY: 0.0606 AC XY: 4510 AN XY: 74432

Gnomad4 AFR AF: 0.0695

Gnomad4 AMR AF: 0.0405

Gnomad4 ASJ AF: 0.0539

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.108

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0337

Gnomad4 OTH AF: 0.0558

Alfa AF: 0.0412 Hom.: 25

Bravo AF: 0.0618

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.53

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

Other links and lift over

dbSNP: rs911886; hg19: chr10-81701580; COSMIC: COSV64852587;