10-79952597-A-G

Position:

• chr10-79952597-A-G

Variant summary

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

The ENST00000444384.3(SFTPD):​c.37-5935T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,066 control chromosomes in the GnomAD database, including 2,068 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 0.15 (2068 hom., cov: 32)
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPD	XM_011540087.2	c.-3-5935T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPD	ENST00000444384.3	c.37-5935T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22227 AN: 151948 Hom.: 2059 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0551

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0617

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.146 AC: 22274 AN: 152066 Hom.: 2068 Cov.: 32 AF XY: 0.151 AC XY: 11221 AN XY: 74326

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.0617

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.158

Alfa AF: 0.121 Hom.: 644

Bravo AF: 0.158

Asia WGS AF: 0.322 AC: 1118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885551; hg19: chr10-81712353;