10-79950053-C-T

Position:

• chr10-79950053-C-T

Variant summary

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

The ENST00000444384.3(SFTPD):​c.37-3391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,974 control chromosomes in the GnomAD database, including 3,131 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 0.18 (3131 hom., cov: 32)
  • Exomes 𝑓: 0.13 (0 hom.)
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.26

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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-3-3391G>A		intron_variant			XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000444384.3	c.37-3391G>A		intron_variant		3		ENSP00000394325.1
ENSG00000283913	ENST00000421889.1	n.359C>T		non_coding_transcript_exon_variant	4/4	3
ENSG00000283913	ENST00000453174.7	n.987C>T		non_coding_transcript_exon_variant	8/8	2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27034 AN: 151832 Hom.: 3131 Cov.: 32

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.0540

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.125 AC: 3 AN: 24 Hom.: 0 Cov.: 0 AF XY: 0.125 AC XY: 2 AN XY: 16

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.178 AC: 27035 AN: 151950 Hom.: 3131 Cov.: 32 AF XY: 0.178 AC XY: 13240 AN XY: 74248

Gnomad4 AFR AF: 0.0506

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.0541

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.172

Alfa AF: 0.211 Hom.: 500

Bravo AF: 0.158

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923536; hg19: chr10-81709809;