chr5-147879583-G-T

Variant names:

• chr5-147879583-G-T
• rs17703574
• NM_054023.5:c.55+725G>T

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+725G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,204 control chromosomes in the GnomAD database, including 635 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 0.066 (635 hom., cov: 33)
• Consequence: SCGB3A2 NM_054023.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_054023.5. 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
	SCGB3A2	NM_054023.5	MANE Select	c.55+725G>T		intron	N/A	NP_473364.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB3A2	ENST00000296694.5	TSL:1 MANE Select	c.55+725G>T		intron	N/A	ENSP00000296694.4
	SCGB3A2	ENST00000504320.5	TSL:3	c.-80-1863G>T		intron	N/A	ENSP00000423930.1
	SCGB3A2	ENST00000507160.5	TSL:3	n.183-1863G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0656 AC: 9979 AN: 152086 Hom.: 634 Cov.: 33

Gnomad AFR AF: 0.0159

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.0478

Gnomad EAS AF: 0.0606

Gnomad SAS AF: 0.0482

Gnomad FIN AF: 0.0895

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0657 AC: 9996 AN: 152204 Hom.: 635 Cov.: 33 AF XY: 0.0694 AC XY: 5163 AN XY: 74420

African (AFR) AF: 0.0158 AC: 657 AN: 41544

American (AMR) AF: 0.206 AC: 3151 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0478 AC: 166 AN: 3470

East Asian (EAS) AF: 0.0607 AC: 314 AN: 5172

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4826

European-Finnish (FIN) AF: 0.0895 AC: 949 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0642 AC: 4367 AN: 68000

Other (OTH) AF: 0.0626 AC: 132 AN: 2110

Alfa AF: 0.0346 Hom.: 28

Bravo AF: 0.0723

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.11
DANN	Benign	0.75
PhyloP100		-1.0
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: rs17703574; hg19: chr5-147259146;