7-116226300-A-G

Position:

• chr7-116226300-A-G

Variant summary

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

The NM_015641.4(TES):​c.28-8234A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 152,128 control chromosomes in the GnomAD database, including 8,923 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 0.33 (8923 hom., cov: 32)
• Consequence: TES NM_015641.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

TES (HGNC:14620): (testin LIM domain protein) Cancer-associated chromosomal changes often involve regions containing fragile sites. This gene maps to a common fragile site on chromosome 7q31.2 designated FRA7G. This gene is similar to mouse Testin, a testosterone-responsive gene encoding a Sertoli cell secretory protein containing three LIM domains. LIM domains are double zinc-finger motifs that mediate protein-protein interactions between transcription factors, cytoskeletal proteins and signaling proteins. This protein is a negative regulator of cell growth and may act as a tumor suppressor. This scaffold protein may also play a role in cell adhesion, cell spreading and in the reorganization of the actin cytoskeleton. Multiple protein isoforms are encoded by transcript variants of this gene.[provided by RefSeq, Aug 2023]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TES	NM_015641.4	c.28-8234A>G		intron_variant		ENST00000358204.9
TES	NM_152829.3	c.-1+3274A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TES	ENST00000358204.9	c.28-8234A>G		intron_variant		1	NM_015641.4	P1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50713 AN: 152010 Hom.: 8891 Cov.: 32

Gnomad AFR AF: 0.434

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.334 AC: 50802 AN: 152128 Hom.: 8923 Cov.: 32 AF XY: 0.340 AC XY: 25273 AN XY: 74376

Gnomad4 AFR AF: 0.435

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.303

Alfa AF: 0.168 Hom.: 312

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.41
DANN	Benign	0.59

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: rs1881287; hg19: chr7-115866354;