20-53212674-G-A

Position:

• chr20-53212674-G-A

Variant summary

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

The NM_173485.6(TSHZ2):​c.41-40825G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.631 in 152,036 control chromosomes in the GnomAD database, including 31,008 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 0.63 (31008 hom., cov: 32)
• Consequence: TSHZ2 NM_173485.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TSHZ2	NM_173485.6	c.41-40825G>A		intron_variant		ENST00000371497.10	NP_775756.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TSHZ2	ENST00000371497.10	c.41-40825G>A		intron_variant		1	NM_173485.6	ENSP00000360552	P1
TSHZ2	ENST00000603338.2	c.31+26998G>A		intron_variant		2		ENSP00000475114

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95901 AN: 151918 Hom.: 30965 Cov.: 32

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.696

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.631 AC: 95992 AN: 152036 Hom.: 31008 Cov.: 32 AF XY: 0.635 AC XY: 47179 AN XY: 74318

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.639

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.621

Alfa AF: 0.556 Hom.: 11803

Bravo AF: 0.647

Asia WGS AF: 0.626 AC: 2180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.035
DANN	Benign	0.47

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: rs1296032; hg19: chr20-51829213;