rs28411392

Positions:

• chr7-116210509-C-T

Variant summary

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

The ENST00000624389.1(ENSG00000279086):​n.1003G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 468,394 control chromosomes in the GnomAD database, including 82,293 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 0.57 (25010 hom., cov: 34)
  • Exomes 𝑓: 0.59 (57283 hom.)
• Consequence: ENST00000624389.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.682

Genes affected

(HGNC:):

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=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TES	NM_015641.4			upstream_gene_variant		ENST00000358204.9	NP_056456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000624389.1	n.1003G>A		non_coding_transcript_exon_variant	1/1
TES	ENST00000358204.9			upstream_gene_variant		1	NM_015641.4	ENSP00000350937	P1

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86255 AN: 151806 Hom.: 24959 Cov.: 34

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.594 AC: 187932 AN: 316480 Hom.: 57283 Cov.: 5 AF XY: 0.593 AC XY: 93598 AN XY: 157890

Gnomad4 AFR exome AF: 0.499

Gnomad4 AMR exome AF: 0.674

Gnomad4 ASJ exome AF: 0.508

Gnomad4 EAS exome AF: 0.879

Gnomad4 SAS exome AF: 0.574

Gnomad4 FIN exome AF: 0.572

Gnomad4 NFE exome AF: 0.577

Gnomad4 OTH exome AF: 0.591

GnomAD4 genome AF: 0.568 AC: 86357 AN: 151914 Hom.: 25010 Cov.: 34 AF XY: 0.575 AC XY: 42684 AN XY: 74262

Gnomad4 AFR AF: 0.495

Gnomad4 AMR AF: 0.636

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.857

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.545

Alfa AF: 0.573 Hom.: 3109

Bravo AF: 0.568

Asia WGS AF: 0.709 AC: 2440 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	15
DANN	Benign	0.91

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: rs28411392; hg19: chr7-115850563;