rs7727031

Positions:

• chr5-147876357-T-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB3A2	ENST00000504320.5	c.-80-5089T>C		intron_variant		3
SCGB3A2	ENST00000507160.5	n.182+4678T>C		intron_variant, non_coding_transcript_variant		3
SCGB3A2	ENST00000514688.1	n.304+4036T>C		intron_variant, non_coding_transcript_variant		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;