rs911886

Variant names:

• chr10-79941824-C-T
• rs911886
• NM_003019.5:c.550+130G>A

Variant summary

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

The ENST00000372292.8(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 ENST00000372292.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13
• Publications: 1 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000372292.8. 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
	SFTPD	NM_003019.5	MANE Select	c.550+130G>A		intron	N/A	NP_003010.4

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTPD	ENST00000372292.8	TSL:1 MANE Select	c.550+130G>A		intron	N/A	ENSP00000361366.3
	SFTPD	ENST00000444384.3	TSL:3	c.589+130G>A		intron	N/A	ENSP00000394325.1
	ENSG00000283913	ENST00000421889.1	TSL:3	n.333+289C>T		intron	N/A

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

African (AFR) AF: 0.0678 AC: 1055 AN: 15570

American (AMR) AF: 0.0262 AC: 839 AN: 32068

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 816 AN: 15658

East Asian (EAS) AF: 0.390 AC: 13828 AN: 35482

South Asian (SAS) AF: 0.0940 AC: 5292 AN: 56268

European-Finnish (FIN) AF: 0.0149 AC: 616 AN: 41426

Middle Eastern (MID) AF: 0.0492 AC: 107 AN: 2176

European-Non Finnish (NFE) AF: 0.0322 AC: 10954 AN: 339806

Other (OTH) AF: 0.0596 AC: 1814 AN: 30434

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

African (AFR) AF: 0.0695 AC: 2887 AN: 41516

American (AMR) AF: 0.0405 AC: 620 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0539 AC: 187 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2007 AN: 5156

South Asian (SAS) AF: 0.108 AC: 520 AN: 4828

European-Finnish (FIN) AF: 0.0138 AC: 146 AN: 10618

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0337 AC: 2289 AN: 68016

Other (OTH) AF: 0.0558 AC: 118 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.53
PhyloP100		-2.1
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: rs911886; hg19: chr10-81701580; COSMIC: COSV64852587;