ENST00000504320.5:c.-81+5285T>A

Variant names:

• chr5-147876039-T-A
• rs7726552
• ENST00000504320.5:c.-81+5285T>A

Variant summary

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

The ENST00000504320.5(SCGB3A2):​c.-81+5285T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.806 in 151,752 control chromosomes in the GnomAD database, including 49,737 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 0.81 (49737 hom., cov: 29)
• Consequence: SCGB3A2 ENST00000504320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 5 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504320.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB3A2	ENST00000504320.5	TSL:3	c.-81+5285T>A		intron	N/A	ENSP00000423930.1
	SCGB3A2	ENST00000507160.5	TSL:3	n.182+4360T>A		intron	N/A
	SCGB3A2	ENST00000514688.1	TSL:3	n.304+3718T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.806 AC: 122265 AN: 151632 Hom.: 49678 Cov.: 29

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.902

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.806 AC: 122386 AN: 151752 Hom.: 49737 Cov.: 29 AF XY: 0.810 AC XY: 60040 AN XY: 74158

African (AFR) AF: 0.883 AC: 36520 AN: 41370

American (AMR) AF: 0.837 AC: 12733 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2712 AN: 3470

East Asian (EAS) AF: 0.902 AC: 4634 AN: 5138

South Asian (SAS) AF: 0.835 AC: 4016 AN: 4812

European-Finnish (FIN) AF: 0.784 AC: 8234 AN: 10506

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.752 AC: 51098 AN: 67938

Other (OTH) AF: 0.796 AC: 1669 AN: 2096

Alfa AF: 0.713 Hom.: 2104

Bravo AF: 0.815

Asia WGS AF: 0.847 AC: 2947 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.066
DANN	Benign	0.44
PhyloP100		-0.92
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: rs7726552; hg19: chr5-147255602;