rs1368408

chr5-147878599-G-A

Variant summary

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

The ENST00000504320.5(SCGB3A2):c.-80-2847G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 576,858 control chromosomes in the GnomAD database, including 10,029 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency:
  • Genomes: 𝑓 0.21 (3788 hom., cov: 32)
  • Exomes 𝑓: 0.16 (6241 hom.)
• Consequence: SCGB3A2 ENST00000504320.5 intron
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: 1.21

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=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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.-80-2847G>A		intron_variant		3
SCGB3A2	ENST00000507160.5	n.183-2847G>A		intron_variant, non_coding_transcript_variant		3
SCGB3A2	ENST00000514688.1	n.305-2847G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31253 AN: 151896 Hom.: 3768 Cov.: 32

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.199

GnomAD4 exome AF: 0.159 AC: 67603 AN: 424844 Hom.: 6241 AF XY: 0.157 AC XY: 34939 AN XY: 223014

Gnomad4 AFR exome AF: 0.306

Gnomad4 AMR exome AF: 0.345

Gnomad4 ASJ exome AF: 0.131

Gnomad4 EAS exome AF: 0.217

Gnomad4 SAS exome AF: 0.140

Gnomad4 FIN exome AF: 0.149

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.162

GnomAD4 genome AF: 0.206 AC: 31322 AN: 152014 Hom.: 3788 Cov.: 32 AF XY: 0.209 AC XY: 15522 AN XY: 74300

Gnomad4 AFR AF: 0.314

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.201

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.206

Alfa AF: 0.151 Hom.: 3923

Bravo AF: 0.222

Asia WGS AF: 0.203 AC: 706 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Inherited susceptibility to asthma Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Mar 01, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	16
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368408; hg19: chr5-147258162;