rs2146192

Variant names:

• chr10-79955982-T-C
• rs2146192
• ENST00000444384.3:c.37-9320A>G

Variant summary

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

The ENST00000444384.3(SFTPD):​c.37-9320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,156 control chromosomes in the GnomAD database, including 2,068 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 0.15 (2068 hom., cov: 33)
• Consequence: SFTPD ENST00000444384.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 10 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTPD	XM_011540087.2	c.-3-9320A>G		intron_variant	Intron 1 of 7		XP_011538389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTPD	ENST00000444384.3	c.37-9320A>G		intron_variant	Intron 1 of 5	3		ENSP00000394325.1

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22253 AN: 152038 Hom.: 2059 Cov.: 33

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.0617

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.147 AC: 22299 AN: 152156 Hom.: 2068 Cov.: 33 AF XY: 0.151 AC XY: 11244 AN XY: 74396

African (AFR) AF: 0.166 AC: 6881 AN: 41498

American (AMR) AF: 0.220 AC: 3355 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 522 AN: 3470

East Asian (EAS) AF: 0.410 AC: 2123 AN: 5172

South Asian (SAS) AF: 0.305 AC: 1473 AN: 4826

European-Finnish (FIN) AF: 0.0617 AC: 653 AN: 10590

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6859 AN: 68000

Other (OTH) AF: 0.158 AC: 334 AN: 2112

Alfa AF: 0.120 Hom.: 5689

Bravo AF: 0.158

Asia WGS AF: 0.322 AC: 1115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.5
DANN	Benign	0.62
PhyloP100		-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2146192; hg19: chr10-81715738;