NM_003019.5:c.751+480G>C

Variant names:

• chr10-79940225-C-G
• rs2819097
• NM_003019.5:c.751+480G>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.751+480G>C		intron_variant	Intron 7 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.751+480G>C		intron_variant	Intron 7 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.634+480G>C		intron_variant	Intron 6 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.751+480G>C		intron_variant	Intron 7 of 7	1	NM_003019.5	ENSP00000361366.3

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

African (AFR) AF: 0.841 AC: 34943 AN: 41542

American (AMR) AF: 0.651 AC: 9941 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3472

East Asian (EAS) AF: 0.778 AC: 4012 AN: 5158

South Asian (SAS) AF: 0.740 AC: 3567 AN: 4822

European-Finnish (FIN) AF: 0.593 AC: 6257 AN: 10560

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40658 AN: 67976

Other (OTH) AF: 0.676 AC: 1424 AN: 2108

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
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2819097; hg19: chr10-81699981;