rs726289

Variant names:

• chr10-79947195-G-A
• rs726289
• NM_003019.5:c.-3-533C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-79947195-G-A
• chr10-79947195-G-T

Variant summary

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

The NM_003019.5(SFTPD):​c.-3-533C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0789 in 152,316 control chromosomes in the GnomAD database, including 632 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 0.079 (632 hom., cov: 33)
• Consequence: SFTPD NM_003019.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910
• Publications: 11 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	NM_003019.5	c.-3-533C>T		intron_variant	Intron 1 of 7	ENST00000372292.8	NP_003010.4
SFTPD	XM_011540087.2	c.-3-533C>T		intron_variant	Intron 1 of 7		XP_011538389.1
SFTPD	XM_011540088.3	c.-3-533C>T		intron_variant	Intron 1 of 6		XP_011538390.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000372292.8	c.-3-533C>T		intron_variant	Intron 1 of 7	1	NM_003019.5	ENSP00000361366.3

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11978 AN: 152198 Hom.: 624 Cov.: 33

Gnomad AFR AF: 0.0633

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.0778

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.0484

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0678

Gnomad OTH AF: 0.0903

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

GnomAD4 genome AF: 0.0789 AC: 12012 AN: 152316 Hom.: 632 Cov.: 33 AF XY: 0.0816 AC XY: 6079 AN XY: 74478

African (AFR) AF: 0.0635 AC: 2638 AN: 41570

American (AMR) AF: 0.176 AC: 2687 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0778 AC: 270 AN: 3470

East Asian (EAS) AF: 0.0170 AC: 88 AN: 5190

South Asian (SAS) AF: 0.201 AC: 967 AN: 4820

European-Finnish (FIN) AF: 0.0484 AC: 514 AN: 10616

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0678 AC: 4616 AN: 68034

Other (OTH) AF: 0.0941 AC: 199 AN: 2114

Alfa AF: 0.0748 Hom.: 747

Bravo AF: 0.0858

Asia WGS AF: 0.128 AC: 445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.71
PhyloP100		0.091
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: rs726289; hg19: chr10-81706951; COSMIC: COSV64852918;