chr11-62422976-C-G

Variant names:

• chr11-62422976-C-G
• rs11231085
• NM_003357.5:c.244-83C>G

Variant summary

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

The NM_003357.5(SCGB1A1):​c.244-83C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 1,303,976 control chromosomes in the GnomAD database, including 72,958 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 0.30 (7230 hom., cov: 32)
  • Exomes 𝑓: 0.33 (65728 hom.)
• Consequence: SCGB1A1 NM_003357.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 14 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]

ENSG00000255446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SCGB1A1	NM_003357.5	c.244-83C>G		intron_variant	Intron 2 of 2	ENST00000278282.3	NP_003348.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SCGB1A1	ENST00000278282.3	c.244-83C>G		intron_variant	Intron 2 of 2	1	NM_003357.5	ENSP00000278282.2
SCGB1A1	ENST00000534397.5	c.139-83C>G		intron_variant	Intron 3 of 3	3		ENSP00000432866.1
ENSG00000255446	ENST00000528983.1	n.39-660G>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45896 AN: 151980 Hom.: 7229 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.307

GnomAD4 exome AF: 0.331 AC: 381570 AN: 1151878 Hom.: 65728 AF XY: 0.326 AC XY: 191421 AN XY: 587560

African (AFR) AF: 0.238 AC: 6471 AN: 27230

American (AMR) AF: 0.324 AC: 14193 AN: 43762

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 7161 AN: 24018

East Asian (EAS) AF: 0.188 AC: 7155 AN: 38124

South Asian (SAS) AF: 0.172 AC: 13675 AN: 79620

European-Finnish (FIN) AF: 0.326 AC: 17046 AN: 52230

Middle Eastern (MID) AF: 0.327 AC: 1689 AN: 5168

European-Non Finnish (NFE) AF: 0.358 AC: 297991 AN: 831904

Other (OTH) AF: 0.325 AC: 16189 AN: 49822

GnomAD4 genome AF: 0.302 AC: 45921 AN: 152098 Hom.: 7230 Cov.: 32 AF XY: 0.296 AC XY: 21973 AN XY: 74356

African (AFR) AF: 0.241 AC: 9983 AN: 41488

American (AMR) AF: 0.325 AC: 4958 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1049 AN: 3466

East Asian (EAS) AF: 0.198 AC: 1022 AN: 5174

South Asian (SAS) AF: 0.152 AC: 735 AN: 4824

European-Finnish (FIN) AF: 0.302 AC: 3194 AN: 10586

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23932 AN: 67976

Other (OTH) AF: 0.304 AC: 641 AN: 2108

Alfa AF: 0.339 Hom.: 1198

Bravo AF: 0.305

Asia WGS AF: 0.183 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.55
PhyloP100		-0.040
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: rs11231085; hg19: chr11-62190448; COSMIC: COSV53473383;