chr10-79945677-C-T

Variant names:

• chr10-79945677-C-T
• rs7078012
• NM_003019.5:c.199+784G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003019.5(SFTPD):​c.199+784G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,092 control chromosomes in the GnomAD database, including 3,775 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 0.20 (3775 hom., cov: 32)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 20 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.199+784G>A		intron_variant	Intron 2 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.199+784G>A		intron_variant	Intron 2 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.199+784G>A		intron_variant	Intron 2 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.199+784G>A		intron_variant	Intron 2 of 7	1	NM_003019.5	ENSP00000361366.3

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30080 AN: 151974 Hom.: 3771 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0395

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.198 AC: 30107 AN: 152092 Hom.: 3775 Cov.: 32 AF XY: 0.194 AC XY: 14464 AN XY: 74370

African (AFR) AF: 0.345 AC: 14315 AN: 41456

American (AMR) AF: 0.173 AC: 2647 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5186

South Asian (SAS) AF: 0.0396 AC: 191 AN: 4826

European-Finnish (FIN) AF: 0.162 AC: 1716 AN: 10580

Middle Eastern (MID) AF: 0.236 AC: 69 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9809 AN: 67970

Other (OTH) AF: 0.203 AC: 427 AN: 2108

Alfa AF: 0.163 Hom.: 6378

Bravo AF: 0.208

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.4
DANN	Benign	0.70
PhyloP100		0.070
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: rs7078012; hg19: chr10-81705433;