10-79951955-T-C

Position:

• chr10-79951955-T-C

Variant summary

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

The ENST00000444384.3(SFTPD):​c.37-5293A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,124 control chromosomes in the GnomAD database, including 7,468 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 0.30 (7468 hom., cov: 33)
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPD	XM_011540087.2	c.-3-5293A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPD	ENST00000444384.3	c.37-5293A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46155 AN: 152004 Hom.: 7466 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.303 AC: 46167 AN: 152124 Hom.: 7468 Cov.: 33 AF XY: 0.303 AC XY: 22527 AN XY: 74368

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.213

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.280

Alfa AF: 0.312 Hom.: 5190

Bravo AF: 0.289

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	9.5
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1885553; hg19: chr10-81711711;