rs17107353

Variant names:

• chr5-147879266-T-A
• rs17107353
• NM_054023.5:c.55+408T>A

Variant summary

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

The NM_054023.5(SCGB3A2):​c.55+408T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,218 control chromosomes in the GnomAD database, including 1,848 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 0.15 (1848 hom., cov: 33)
• Consequence: SCGB3A2 NM_054023.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132
• Publications: 2 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=-0.7).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCGB3A2	NM_054023.5	c.55+408T>A		intron_variant	Intron 1 of 2	ENST00000296694.5	NP_473364.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCGB3A2	ENST00000296694.5	c.55+408T>A		intron_variant	Intron 1 of 2	1	NM_054023.5	ENSP00000296694.4
SCGB3A2	ENST00000504320.5	c.-80-2180T>A		intron_variant	Intron 1 of 2	3		ENSP00000423930.1
SCGB3A2	ENST00000507160.5	n.183-2180T>A		intron_variant	Intron 1 of 2	3
SCGB3A2	ENST00000514688.1	n.305-2180T>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22190 AN: 152098 Hom.: 1846 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.146 AC: 22231 AN: 152218 Hom.: 1848 Cov.: 33 AF XY: 0.149 AC XY: 11091 AN XY: 74408

African (AFR) AF: 0.127 AC: 5260 AN: 41536

American (AMR) AF: 0.271 AC: 4136 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 461 AN: 3472

East Asian (EAS) AF: 0.115 AC: 597 AN: 5174

South Asian (SAS) AF: 0.112 AC: 540 AN: 4822

European-Finnish (FIN) AF: 0.155 AC: 1642 AN: 10594

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9181 AN: 68016

Other (OTH) AF: 0.159 AC: 337 AN: 2116

Alfa AF: 0.155 Hom.: 239

Bravo AF: 0.153

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	6.0
DANN	Benign	0.81
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs17107353; hg19: chr5-147258829;