20-53113713-C-T

Variant names:

• chr20-53113713-C-T
• rs1936958
• NM_173485.6:c.41-139786C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173485.6(TSHZ2):​c.41-139786C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0694 in 152,206 control chromosomes in the GnomAD database, including 846 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 0.069 (846 hom., cov: 32)
• Consequence: TSHZ2 NM_173485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.133

Genes affected

TSHZ2 (HGNC:13010): (teashirt zinc finger homeobox 2) This gene is a member of the teashirt C2H2-type zinc-finger protein family of transcription factors. This gene encodes a protein with five C2H2-type zinc fingers, a homeobox DNA-binding domain and a coiled-coil domain. This nuclear protein is predicted to act as a transcriptional repressor. This gene is thought to play a role in the development and progression of breast and other types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSHZ2	NM_173485.6	c.41-139786C>T		intron_variant	Intron 1 of 2	ENST00000371497.10	NP_775756.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TSHZ2	ENST00000371497.10	c.41-139786C>T		intron_variant	Intron 1 of 2	1	NM_173485.6	ENSP00000360552.3

Frequencies

GnomAD3 genomes AF: 0.0693 AC: 10540 AN: 152088 Hom.: 845 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0328

Gnomad ASJ AF: 0.0389

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.0469

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0694 AC: 10558 AN: 152206 Hom.: 846 Cov.: 32 AF XY: 0.0747 AC XY: 5556 AN XY: 74426

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.0327

Gnomad4 ASJ AF: 0.0389

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.0469

Gnomad4 NFE AF: 0.0187

Gnomad4 OTH AF: 0.0738

Alfa AF: 0.0499 Hom.: 54

Bravo AF: 0.0663

Asia WGS AF: 0.282 AC: 977 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.73

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: rs1936958; hg19: chr20-51730252;