rs2245121

chr10-79939482-G-A

Variant summary

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

The NM_003019.5(SFTPD):c.751+1223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,140 control chromosomes in the GnomAD database, including 18,426 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 0.48 (18426 hom., cov: 33)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTPD	NM_003019.5	c.751+1223C>T		intron_variant		ENST00000372292.8
SFTPD	XM_011540087.2	c.751+1223C>T		intron_variant
SFTPD	XM_011540088.3	c.634+1223C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTPD	ENST00000372292.8	c.751+1223C>T		intron_variant		1	NM_003019.5	P1
	ENST00000421889.1	n.235-1955G>A		intron_variant, non_coding_transcript_variant		3
SFTPD	ENST00000678361.1	n.2956+1223C>T		intron_variant, non_coding_transcript_variant
SFTPD	ENST00000679234.1	n.2877+1223C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73057 AN: 152022 Hom.: 18414 Cov.: 33

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.481 AC: 73110 AN: 152140 Hom.: 18426 Cov.: 33 AF XY: 0.482 AC XY: 35849 AN XY: 74352

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.447

Alfa AF: 0.428 Hom.: 12840

Bravo AF: 0.475

Asia WGS AF: 0.588 AC: 2045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.034
Dann	Benign	0.61

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: rs2245121; hg19: chr10-81699238;