11-62415535-C-T

Variant names:

• chr11-62415535-C-T
• rs10897270
• ENST00000534397.5:c.-124-1029C>T

Variant summary

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

The ENST00000534397.5(SCGB1A1):​c.-124-1029C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 149,208 control chromosomes in the GnomAD database, including 29,070 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 0.61 (29070 hom., cov: 30)
• Consequence: SCGB1A1 ENST00000534397.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639
• Publications: 11 publications found

Genes affected

SCGB1A1 (HGNC:12523): (secretoglobin family 1A member 1) This gene encodes a member of the secretoglobin family of small secreted proteins. The encoded protein has been implicated in numerous functions including anti-inflammation, inhibition of phospholipase A2 and the sequestering of hydrophobic ligands. Defects in this gene are associated with a susceptibility to asthma. [provided by RefSeq, May 2010]

LOC102723765 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000534397.5. 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
	SCGB1A1	ENST00000534397.5	TSL:3	c.-124-1029C>T		intron	N/A	ENSP00000432866.1

Frequencies

GnomAD3 genomes AF: 0.610 AC: 90973 AN: 149088 Hom.: 29029 Cov.: 30

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.610 AC: 91068 AN: 149208 Hom.: 29070 Cov.: 30 AF XY: 0.612 AC XY: 44649 AN XY: 73004

African (AFR) AF: 0.691 AC: 26774 AN: 38732

American (AMR) AF: 0.631 AC: 9615 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2049 AN: 3466

East Asian (EAS) AF: 0.560 AC: 2885 AN: 5152

South Asian (SAS) AF: 0.469 AC: 2262 AN: 4820

European-Finnish (FIN) AF: 0.657 AC: 6951 AN: 10572

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38541 AN: 67938

Other (OTH) AF: 0.632 AC: 1325 AN: 2096

Alfa AF: 0.574 Hom.: 15832

Bravo AF: 0.620

Asia WGS AF: 0.553 AC: 1920 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.51
DANN	Benign	0.32
PhyloP100		-0.64
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: rs10897270; hg19: chr11-62183007;