5-147876039-T-A

Position:

• chr5-147876039-T-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB3A2	ENST00000504320.5	c.-81+5285T>A		intron_variant		3
SCGB3A2	ENST00000507160.5	n.182+4360T>A		intron_variant, non_coding_transcript_variant		3
SCGB3A2	ENST00000514688.1	n.304+3718T>A		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.782

Gnomad4 EAS AF: 0.902

Gnomad4 SAS AF: 0.835

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.796

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.066
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7726552; hg19: chr5-147255602;