rs1998374

chr10-79942966-T-Cchr10-79942966-T-G

Variant summary

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

The NM_003019.5(SFTPD):c.200-87A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 838,808 control chromosomes in the GnomAD database, including 14,320 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 (3221 hom., cov: 32)
  • Exomes 𝑓: 0.15 (11099 hom.)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.596

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPD	NM_003019.5	c.200-87A>G		intron_variant		ENST00000372292.8
SFTPD	XM_011540087.2	c.200-87A>G		intron_variant
SFTPD	XM_011540088.3	c.200-87A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPD	ENST00000372292.8	c.200-87A>G		intron_variant		1	NM_003019.5	P1

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27613 AN: 151948 Hom.: 3208 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.174

GnomAD4 exome AF: 0.151 AC: 103807 AN: 686742 Hom.: 11099 AF XY: 0.155 AC XY: 56681 AN XY: 366614

Gnomad4 AFR exome AF: 0.288

Gnomad4 AMR exome AF: 0.272

Gnomad4 ASJ exome AF: 0.172

Gnomad4 EAS exome AF: 0.422

Gnomad4 SAS exome AF: 0.276

Gnomad4 FIN exome AF: 0.0699

Gnomad4 NFE exome AF: 0.0997

Gnomad4 OTH exome AF: 0.159

GnomAD4 genome AF: 0.182 AC: 27675 AN: 152066 Hom.: 3221 Cov.: 32 AF XY: 0.185 AC XY: 13782 AN XY: 74342

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.410

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.0619

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.180

Alfa AF: 0.0793 Hom.: 134

Bravo AF: 0.199

Asia WGS AF: 0.332 AC: 1151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.9
Dann	Benign	0.80

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: rs1998374; hg19: chr10-81702722;