NM_006292.4:c.42+139A>T

Variant names:

• chr11-18526636-T-A
• rs1395319
• NM_006292.4:c.42+139A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_006292.4(TSG101):​c.42+139A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TSG101 NM_006292.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0820
• Publications: 0 publications found

Genes affected

TSG101 (HGNC:15971): (tumor susceptibility 101) The protein encoded by this gene belongs to a group of apparently inactive homologs of ubiquitin-conjugating enzymes. The gene product contains a coiled-coil domain that interacts with stathmin, a cytosolic phosphoprotein implicated in tumorigenesis. The protein may play a role in cell growth and differentiation and act as a negative growth regulator. In vitro steady-state expression of this tumor susceptibility gene appears to be important for maintenance of genomic stability and cell cycle regulation. Mutations and alternative splicing in this gene occur in high frequency in breast cancer and suggest that defects occur during breast cancer tumorigenesis and/or progression. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSG101	NM_006292.4	c.42+139A>T		intron_variant	Intron 1 of 9	ENST00000251968.4	NP_006283.1
TSG101	XM_005253108.5	c.-157+139A>T		intron_variant	Intron 1 of 10		XP_005253165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSG101	ENST00000251968.4	c.42+139A>T		intron_variant	Intron 1 of 9	1	NM_006292.4	ENSP00000251968.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 845310 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 424288

African (AFR) AF: 0.00 AC: 0 AN: 19346

American (AMR) AF: 0.00 AC: 0 AN: 18996

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16058

East Asian (EAS) AF: 0.00 AC: 0 AN: 30768

South Asian (SAS) AF: 0.00 AC: 0 AN: 55160

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29840

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2784

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 633580

Other (OTH) AF: 0.00 AC: 0 AN: 38778

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	10
DANN	Benign	0.18
PhyloP100		0.082
PromoterAI		0.083	Neutral

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: rs1395319; hg19: chr11-18548183;