rs4902467

chr14-36489822-A-Gchr14-36489822-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_161364.1(SFTA3):n.180+1379T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,170 control chromosomes in the GnomAD database, including 4,568 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 (4568 hom., cov: 32)
• Consequence: SFTA3 NR_161364.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.399 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SFTA3	NR_161364.1	n.180+1379T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFTA3	ENST00000518529.6	n.809+1379T>C		intron_variant, non_coding_transcript_variant		1
	ENST00000634305.1	n.322+40985A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33710 AN: 152052 Hom.: 4564 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.222 AC: 33731 AN: 152170 Hom.: 4568 Cov.: 32 AF XY: 0.228 AC XY: 16943 AN XY: 74396

Gnomad4 AFR AF: 0.0649

Gnomad4 AMR AF: 0.322

Gnomad4 ASJ AF: 0.277

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.233

Alfa AF: 0.252 Hom.: 2234

Bravo AF: 0.217

Asia WGS AF: 0.340 AC: 1179 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.0
Dann	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs4902467; hg19: chr14-36959027;