ENST00000504320.5:c.-80-5089T>C

Variant names:

• chr5-147876357-T-C
• rs7727031
• ENST00000504320.5:c.-80-5089T>C

Variant summary

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

The ENST00000504320.5(SCGB3A2):​c.-80-5089T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 151,940 control chromosomes in the GnomAD database, including 2,344 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 0.14 (2344 hom., cov: 31)
• Consequence: SCGB3A2 ENST00000504320.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB3A2	ENST00000504320.5	TSL:3	c.-80-5089T>C		intron	N/A	ENSP00000423930.1
	SCGB3A2	ENST00000507160.5	TSL:3	n.182+4678T>C		intron	N/A
	SCGB3A2	ENST00000514688.1	TSL:3	n.304+4036T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20767 AN: 151822 Hom.: 2332 Cov.: 31

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0814

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0561

Gnomad SAS AF: 0.0606

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.137 AC: 20812 AN: 151940 Hom.: 2344 Cov.: 31 AF XY: 0.135 AC XY: 10044 AN XY: 74234

African (AFR) AF: 0.311 AC: 12853 AN: 41354

American (AMR) AF: 0.0812 AC: 1240 AN: 15270

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

East Asian (EAS) AF: 0.0558 AC: 287 AN: 5140

South Asian (SAS) AF: 0.0606 AC: 292 AN: 4818

European-Finnish (FIN) AF: 0.0650 AC: 688 AN: 10578

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4831 AN: 67994

Other (OTH) AF: 0.129 AC: 272 AN: 2108

Alfa AF: 0.0933 Hom.: 1668

Bravo AF: 0.147

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.56
PhyloP100		0.28
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: rs7727031; hg19: chr5-147255920;