chr5-147876357-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.306 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.-80-5089T>C		intron_variant	Intron 1 of 2	3		ENSP00000423930.1
SCGB3A2	ENST00000507160.5	n.182+4678T>C		intron_variant	Intron 1 of 2	3
SCGB3A2	ENST00000514688.1	n.304+4036T>C		intron_variant	Intron 1 of 2	3

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

Gnomad4 AFR AF: 0.311

Gnomad4 AMR AF: 0.0812

Gnomad4 ASJ AF: 0.0850

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.0606

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0865 Hom.: 1032

Bravo AF: 0.147

Asia WGS AF: 0.0600 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.8
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7727031; hg19: chr5-147255920;