rs3741240

Variant names:

• chr11-62419070-G-A
• rs3741240
• NM_003357.5:c.-26G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-62419070-G-A
• chr11-62419070-G-C
• chr11-62419070-G-T

Variant summary

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

The NM_003357.5(SCGB1A1):​c.-26G>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 0.346 in 1,564,120 control chromosomes in the GnomAD database, including 95,587 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency:
  • Genomes: 𝑓 0.32 (7916 hom., cov: 31)
  • Exomes 𝑓: 0.35 (87671 hom.)
• Consequence: SCGB1A1 NM_003357.5 5_prime_UTR
• Clinical Significance: association no assertion criteria provided O:1
• Conservation: PhyloP100: -0.268
• Publications: 102 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003357.5. 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
	SCGB1A1	NM_003357.5	MANE Select	c.-26G>A		5_prime_UTR	Exon 1 of 3	NP_003348.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SCGB1A1	ENST00000278282.3	TSL:1 MANE Select	c.-26G>A		5_prime_UTR	Exon 1 of 3	ENSP00000278282.2
	SCGB1A1	ENST00000534397.5	TSL:3	c.-51+2433G>A		intron	N/A	ENSP00000432866.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48666 AN: 151822 Hom.: 7909 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.300

GnomAD2 exomes AF: 0.340 AC: 76958 AN: 226384 AF XY: 0.349

Gnomad AFR exome AF: 0.242

Gnomad AMR exome AF: 0.259

Gnomad ASJ exome AF: 0.321

Gnomad EAS exome AF: 0.358

Gnomad FIN exome AF: 0.350

Gnomad NFE exome AF: 0.340

Gnomad OTH exome AF: 0.323

GnomAD4 exome AF: 0.349 AC: 492525 AN: 1412180 Hom.: 87671 Cov.: 31 AF XY: 0.353 AC XY: 247396 AN XY: 701130

African (AFR) AF: 0.246 AC: 7791 AN: 31682

American (AMR) AF: 0.258 AC: 10485 AN: 40592

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 7899 AN: 24618

East Asian (EAS) AF: 0.383 AC: 14338 AN: 37472

South Asian (SAS) AF: 0.464 AC: 36244 AN: 78038

European-Finnish (FIN) AF: 0.348 AC: 18187 AN: 52308

Middle Eastern (MID) AF: 0.259 AC: 1446 AN: 5576

European-Non Finnish (NFE) AF: 0.347 AC: 376345 AN: 1083780

Other (OTH) AF: 0.341 AC: 19790 AN: 58114

GnomAD4 genome AF: 0.320 AC: 48693 AN: 151940 Hom.: 7916 Cov.: 31 AF XY: 0.323 AC XY: 24016 AN XY: 74264

African (AFR) AF: 0.254 AC: 10515 AN: 41434

American (AMR) AF: 0.295 AC: 4505 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3470

East Asian (EAS) AF: 0.370 AC: 1906 AN: 5152

South Asian (SAS) AF: 0.484 AC: 2326 AN: 4804

European-Finnish (FIN) AF: 0.360 AC: 3803 AN: 10564

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23563 AN: 67954

Other (OTH) AF: 0.304 AC: 639 AN: 2100

Alfa AF: 0.334 Hom.: 28188

Bravo AF: 0.304

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Chronic obstructive pulmonary disease (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.18
DANN	Benign	0.48
PhyloP100		-0.27
PromoterAI		0.0062	Neutral
Mutation Taster		=300/0	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: rs3741240; hg19: chr11-62186542; COSMIC: COSV53473598; COSMIC: COSV53473598;