chr10-79944096-C-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.200-1217G>C		intron_variant	Intron 2 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.200-1217G>C		intron_variant	Intron 2 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.200-1217G>C		intron_variant	Intron 2 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.200-1217G>C		intron_variant	Intron 2 of 7	1	NM_003019.5	ENSP00000361366.3

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

Gnomad4 AFR AF: 0.0607

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0783

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0482

Gnomad4 NFE AF: 0.0677

Gnomad4 OTH AF: 0.0918

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.43

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: rs17886286; hg19: chr10-81703852;