NM_139022.3:c.355-1209A>G

Variant names:

• chr11-2312445-A-G
• rs800140
• NM_139022.3:c.355-1209A>G

Variant summary

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

The NM_139022.3(TSPAN32):​c.355-1209A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.577 in 152,208 control chromosomes in the GnomAD database, including 29,169 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 0.58 (29169 hom., cov: 35)
• Consequence: TSPAN32 NM_139022.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 12 publications found

Genes affected

TSPAN32 (HGNC:13410): (tetraspanin 32) This gene, which is a member of the tetraspanin superfamily, is one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of chromosome 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian and breast cancers. This gene is located among several imprinted genes; however, this gene, as well as the tumor-suppressing subchromosomal transferable fragment 4, escapes imprinting. This gene may play a role in malignancies and diseases that involve this region, and it is also involved in hematopoietic cell function. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]

LOC124902612 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.759 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSPAN32	NM_139022.3	c.355-1209A>G		intron_variant	Intron 4 of 9	ENST00000182290.9	NP_620591.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSPAN32	ENST00000182290.9	c.355-1209A>G		intron_variant	Intron 4 of 9	1	NM_139022.3	ENSP00000182290.5

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87757 AN: 152090 Hom.: 29173 Cov.: 35

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.577 AC: 87754 AN: 152208 Hom.: 29169 Cov.: 35 AF XY: 0.572 AC XY: 42568 AN XY: 74398

African (AFR) AF: 0.245 AC: 10193 AN: 41540

American (AMR) AF: 0.573 AC: 8762 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2386 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1980 AN: 5164

South Asian (SAS) AF: 0.686 AC: 3314 AN: 4830

European-Finnish (FIN) AF: 0.647 AC: 6853 AN: 10586

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 52010 AN: 68010

Other (OTH) AF: 0.616 AC: 1300 AN: 2110

Alfa AF: 0.721 Hom.: 20622

Bravo AF: 0.554

Asia WGS AF: 0.554 AC: 1932 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.57
PhyloP100		-1.2
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: rs800140; hg19: chr11-2333675;