10-79944096-C-G

Variant names:

• chr10-79944096-C-G
• rs17886286
• NM_003019.5:c.200-1217G>C

Variant summary

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

The NM_003019.5(SFTPD):​c.200-1217G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.073 in 152,250 control chromosomes in the GnomAD database, including 494 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 0.073 (494 hom., cov: 32)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003019.5. 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.200-1217G>C		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.200-1217G>C		intron	N/A	ENSP00000361366.3
	SFTPD	ENST00000678361.1		n.613G>C		non_coding_transcript_exon	Exon 1 of 4
	SFTPD	ENST00000679234.1		n.851G>C		non_coding_transcript_exon	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.0728 AC: 11080 AN: 152132 Hom.: 489 Cov.: 32

Gnomad AFR AF: 0.0603

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.0783

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0482

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0677

Gnomad OTH AF: 0.0880

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0730 AC: 11114 AN: 152250 Hom.: 494 Cov.: 32 AF XY: 0.0751 AC XY: 5591 AN XY: 74450

African (AFR) AF: 0.0607 AC: 2522 AN: 41558

American (AMR) AF: 0.127 AC: 1935 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0783 AC: 272 AN: 3472

East Asian (EAS) AF: 0.0141 AC: 73 AN: 5166

South Asian (SAS) AF: 0.200 AC: 968 AN: 4830

European-Finnish (FIN) AF: 0.0482 AC: 512 AN: 10612

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

European-Non Finnish (NFE) AF: 0.0677 AC: 4605 AN: 68010

Other (OTH) AF: 0.0918 AC: 194 AN: 2114

Alfa AF: 0.0245 Hom.: 16

Bravo AF: 0.0750

Asia WGS AF: 0.125 AC: 434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.43
PhyloP100		-1.1
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: rs17886286; hg19: chr10-81703852;