rs2107332

Variant names:

• chr20-53218826-T-C
• rs2107332
• NM_173485.6:c.41-34673T>C

Variant summary

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

The NM_173485.6(TSHZ2):​c.41-34673T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0787 in 152,280 control chromosomes in the GnomAD database, including 559 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 0.079 (559 hom., cov: 33)
• Consequence: TSHZ2 NM_173485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.14
• Publications: 0 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TSHZ2	NM_173485.6	c.41-34673T>C		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.41-34673T>C		intron_variant	Intron 1 of 2	1	NM_173485.6	ENSP00000360552.3
TSHZ2	ENST00000603338.2	c.31+33150T>C		intron_variant	Intron 1 of 2	2		ENSP00000475114.1

Frequencies

GnomAD3 genomes AF: 0.0787 AC: 11977 AN: 152162 Hom.: 558 Cov.: 33

Gnomad AFR AF: 0.0300

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0856

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0787 AC: 11981 AN: 152280 Hom.: 559 Cov.: 33 AF XY: 0.0787 AC XY: 5861 AN XY: 74444

African (AFR) AF: 0.0301 AC: 1252 AN: 41554

American (AMR) AF: 0.0631 AC: 965 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 435 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0863 AC: 417 AN: 4830

European-Finnish (FIN) AF: 0.125 AC: 1318 AN: 10586

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7132 AN: 68030

Other (OTH) AF: 0.0929 AC: 196 AN: 2110

Alfa AF: 0.0909 Hom.: 590

Bravo AF: 0.0716

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		1.1
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: rs2107332; hg19: chr20-51835365;