14-36488976-A-G

Variant names:

• chr14-36488976-A-G
• rs35852547
• ENST00000518529.6:n.809+2225T>C

Variant summary

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

The ENST00000518529.6(SFTA3):​n.809+2225T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,186 control chromosomes in the GnomAD database, including 4,510 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 0.22 (4510 hom., cov: 32)
• Consequence: SFTA3 ENST00000518529.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 2 publications found

Genes affected

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

SFTA3 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SFTA3	NR_138597.1	n.765+2225T>C		intron_variant	Intron 2 of 4
SFTA3	NR_138598.1	n.765+2225T>C		intron_variant	Intron 2 of 5
SFTA3	NR_138599.1	n.765+2225T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFTA3	ENST00000546983.2	n.*53+2225T>C		intron_variant	Intron 3 of 3	4		ENSP00000449302.2

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33066 AN: 152066 Hom.: 4506 Cov.: 32

Gnomad AFR AF: 0.0519

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.217 AC: 33085 AN: 152186 Hom.: 4510 Cov.: 32 AF XY: 0.224 AC XY: 16654 AN XY: 74410

African (AFR) AF: 0.0518 AC: 2154 AN: 41558

American (AMR) AF: 0.320 AC: 4898 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 961 AN: 3472

East Asian (EAS) AF: 0.412 AC: 2130 AN: 5168

South Asian (SAS) AF: 0.262 AC: 1267 AN: 4830

European-Finnish (FIN) AF: 0.298 AC: 3158 AN: 10596

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.261 AC: 17767 AN: 67964

Other (OTH) AF: 0.229 AC: 482 AN: 2104

Alfa AF: 0.245 Hom.: 892

Bravo AF: 0.213

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.73
PhyloP100		0.67
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: rs35852547; hg19: chr14-36958181;