14-36506369-C-T

Variant names:

• chr14-36506369-C-T
• rs1005343
• ENST00000518529.6:n.718+6743G>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+12616G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.939 in 152,216 control chromosomes in the GnomAD database, including 67,524 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 0.94 (67524 hom., cov: 32)
• Consequence: SFTA3 ENST00000546983.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 0 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=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546983.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTA3	NR_138597.1		n.674+6743G>A		intron	N/A
	SFTA3	NR_138598.1		n.674+6743G>A		intron	N/A
	SFTA3	NR_138599.1		n.674+6743G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SFTA3	ENST00000518529.6	TSL:1	n.718+6743G>A		intron	N/A
	SFTA3	ENST00000521114.5	TSL:1	n.420+6743G>A		intron	N/A
	SFTA3	ENST00000546983.2	TSL:4	n.373+12616G>A		intron	N/A	ENSP00000449302.2

Frequencies

GnomAD3 genomes AF: 0.939 AC: 142832 AN: 152098 Hom.: 67486 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.990

Gnomad FIN AF: 0.977

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.990

Gnomad OTH AF: 0.950

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

GnomAD4 genome AF: 0.939 AC: 142926 AN: 152216 Hom.: 67524 Cov.: 32 AF XY: 0.941 AC XY: 70058 AN XY: 74430

African (AFR) AF: 0.819 AC: 33999 AN: 41490

American (AMR) AF: 0.970 AC: 14844 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3217 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5159 AN: 5170

South Asian (SAS) AF: 0.990 AC: 4777 AN: 4824

European-Finnish (FIN) AF: 0.977 AC: 10380 AN: 10622

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.990 AC: 67347 AN: 68020

Other (OTH) AF: 0.950 AC: 2009 AN: 2114

Alfa AF: 0.913 Hom.: 25250

Bravo AF: 0.932

Asia WGS AF: 0.978 AC: 3399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.86
PhyloP100		0.38
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: rs1005343; hg19: chr14-36975574;