rs41364547

Positions:

• chr11-62419058-G-A

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_003357.5(SCGB1A1):​c.-38G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000888 in 1,553,694 control chromosomes in the GnomAD database, including 11 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 0.0032 (3 hom., cov: 32)
  • Exomes 𝑓: 0.00064 (8 hom.)
• Consequence: SCGB1A1 NM_003357.5 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82

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

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCGB1A1	NM_003357.5	c.-38G>A		5_prime_UTR_variant	1/3	ENST00000278282.3
LOC102723765	XR_007062699.1	n.238-2208C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCGB1A1	ENST00000278282.3	c.-38G>A		5_prime_UTR_variant	1/3	1	NM_003357.5	P1
SCGB1A1	ENST00000534397.5	c.-51+2421G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00316 AC: 481 AN: 152134 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00968

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00151

Gnomad ASJ AF: 0.0112

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.00430

GnomAD3 exomes AF: 0.00145 AC: 322 AN: 221718 Hom.: 1 AF XY: 0.00118 AC XY: 142 AN XY: 119842

Gnomad AFR exome AF: 0.00951

Gnomad AMR exome AF: 0.00132

Gnomad ASJ exome AF: 0.0141

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000137

Gnomad OTH exome AF: 0.00154

GnomAD4 exome AF: 0.000637 AC: 893 AN: 1401442 Hom.: 8 Cov.: 27 AF XY: 0.000634 AC XY: 441 AN XY: 695100

Gnomad4 AFR exome AF: 0.0100

Gnomad4 AMR exome AF: 0.00127

Gnomad4 ASJ exome AF: 0.0127

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000105

Gnomad4 OTH exome AF: 0.00187

GnomAD4 genome AF: 0.00319 AC: 486 AN: 152252 Hom.: 3 Cov.: 32 AF XY: 0.00299 AC XY: 223 AN XY: 74464

Gnomad4 AFR AF: 0.00977

Gnomad4 AMR AF: 0.00151

Gnomad4 ASJ AF: 0.0112

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.00426

Alfa AF: 0.00252 Hom.: 1

Bravo AF: 0.00352

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.29
DANN	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs41364547; hg19: chr11-62186530; COSMIC: COSV53473491; COSMIC: COSV53473491;