rs2819097

Positions:

• chr10-79940225-C-G

Variant summary

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

The NM_003019.5(SFTPD):​c.751+480G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,124 control chromosomes in the GnomAD database, including 36,333 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 0.68 (36333 hom., cov: 33)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.751+480G>C		intron_variant		ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.751+480G>C		intron_variant			XP_011538389.1
SFTPD	XM_011540088.3	c.634+480G>C		intron_variant			XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.751+480G>C		intron_variant		1	NM_003019.5	ENSP00000361366	P1
	ENST00000421889.1	n.235-1212C>G		intron_variant, non_coding_transcript_variant		3
SFTPD	ENST00000678361.1	n.2956+480G>C		intron_variant, non_coding_transcript_variant
SFTPD	ENST00000679234.1	n.2877+480G>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103657 AN: 152006 Hom.: 36265 Cov.: 33

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.682 AC: 103792 AN: 152124 Hom.: 36333 Cov.: 33 AF XY: 0.684 AC XY: 50847 AN XY: 74340

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.676

Alfa AF: 0.648 Hom.: 4044

Bravo AF: 0.690

Asia WGS AF: 0.774 AC: 2693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.16
DANN	Benign	0.53

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: rs2819097; hg19: chr10-81699981;