rs999460

Variant names:

• chr14-36515306-C-T
• rs999460
• ENST00000546983.2:n.373+3679G>A

Variant summary

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

The ENST00000546983.2(SFTA3):​n.373+3679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,216 control chromosomes in the GnomAD database, including 6,047 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 0.25 (6047 hom., cov: 33)
• Consequence: SFTA3 ENST00000546983.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.364
• Publications: 8 publications found

Genes affected

SFTA3 (HGNC:):

SFTA3 (HGNC:18387): (surfactant associated 3) Involved in wound healing. Located in cytoplasm and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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 (NFE) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTA3	NR_161364.1	n.89+4162G>A		intron_variant	Intron 1 of 4
SFTA3	NR_161365.1	n.89+4162G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTA3	ENST00000546983.2	n.373+3679G>A		intron_variant	Intron 2 of 3	4		ENSP00000449302.2
SFTA3	ENST00000521945.1	n.54+4162G>A		intron_variant	Intron 1 of 4	2
ENSG00000283098	ENST00000634305.1	n.322+66469C>T		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38116 AN: 152098 Hom.: 6047 Cov.: 33

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.0630

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.250 AC: 38118 AN: 152216 Hom.: 6047 Cov.: 33 AF XY: 0.244 AC XY: 18177 AN XY: 74408

African (AFR) AF: 0.0822 AC: 3417 AN: 41560

American (AMR) AF: 0.246 AC: 3756 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.307 AC: 1064 AN: 3470

East Asian (EAS) AF: 0.0626 AC: 324 AN: 5178

South Asian (SAS) AF: 0.161 AC: 776 AN: 4818

European-Finnish (FIN) AF: 0.297 AC: 3142 AN: 10586

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24617 AN: 67986

Other (OTH) AF: 0.284 AC: 601 AN: 2116

Alfa AF: 0.319 Hom.: 5522

Bravo AF: 0.237

Asia WGS AF: 0.124 AC: 437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.5
DANN	Benign	0.64
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs999460; hg19: chr14-36984511;