rs6882292

Variant names:

• chr5-147877993-G-A
• rs6882292
• ENST00000504320.5:c.-80-3453G>A

Variant summary

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

The ENST00000504320.5(SCGB3A2):​c.-80-3453G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0727 in 152,206 control chromosomes in the GnomAD database, including 421 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 0.073 (421 hom., cov: 33)
• Consequence: SCGB3A2 ENST00000504320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 7 publications found

Genes affected

SCGB3A2 (HGNC:18391): (secretoglobin family 3A member 2) The protein encoded by this gene is a secreted lung surfactant protein and a downstream target of thyroid transcription factor. A single nucleotide polymorphism in the promoter of this gene results in susceptibility to asthma.[provided by RefSeq, Mar 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCGB3A2	ENST00000504320.5	c.-80-3453G>A		intron_variant	Intron 1 of 2	3		ENSP00000423930.1
SCGB3A2	ENST00000507160.5	n.183-3453G>A		intron_variant	Intron 1 of 2	3
SCGB3A2	ENST00000514688.1	n.305-3453G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.0727 AC: 11055 AN: 152088 Hom.: 422 Cov.: 33

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0600

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0706

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0727 AC: 11068 AN: 152206 Hom.: 421 Cov.: 33 AF XY: 0.0716 AC XY: 5326 AN XY: 74420

African (AFR) AF: 0.0851 AC: 3532 AN: 41524

American (AMR) AF: 0.0611 AC: 934 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.0556 AC: 288 AN: 5178

South Asian (SAS) AF: 0.0599 AC: 289 AN: 4826

European-Finnish (FIN) AF: 0.0653 AC: 692 AN: 10592

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0706 AC: 4800 AN: 67996

Other (OTH) AF: 0.0880 AC: 186 AN: 2114

Alfa AF: 0.0753 Hom.: 140

Bravo AF: 0.0725

Asia WGS AF: 0.0440 AC: 154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.46
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6882292; hg19: chr5-147257556;