rs200640

Positions:

• chr20-53288170-A-G

Variant summary

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

The NM_173485.6(TSHZ2):​c.*8+31599A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,178 control chromosomes in the GnomAD database, including 726 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 0.086 (726 hom., cov: 31)
• Consequence: TSHZ2 NM_173485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSHZ2	NM_173485.6	c.*8+31599A>G		intron_variant		ENST00000371497.10	NP_775756.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSHZ2	ENST00000371497.10	c.*8+31599A>G		intron_variant		1	NM_173485.6	ENSP00000360552	P1
	ENST00000606932.1	n.134-14789T>C		intron_variant, non_coding_transcript_variant		5
TSHZ2	ENST00000603338.2	c.*8+31599A>G		intron_variant		2		ENSP00000475114
TSHZ2	ENST00000605656.2	c.*8+31599A>G		intron_variant, NMD_transcript_variant		4		ENSP00000474159

Frequencies

GnomAD3 genomes AF: 0.0862 AC: 13113 AN: 152060 Hom.: 718 Cov.: 31

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0956

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0762

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0986

Gnomad OTH AF: 0.0971

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

GnomAD4 genome AF: 0.0863 AC: 13135 AN: 152178 Hom.: 726 Cov.: 31 AF XY: 0.0860 AC XY: 6398 AN XY: 74372

Gnomad4 AFR AF: 0.0377

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0762

Gnomad4 NFE AF: 0.0986

Gnomad4 OTH AF: 0.104

Alfa AF: 0.0852 Hom.: 73

Bravo AF: 0.0868

Asia WGS AF: 0.176 AC: 613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	7.1
DANN	Benign	0.84

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: rs200640; hg19: chr20-51904709;