chr7-116210706-A-G

Variant names:

• chr7-116210706-A-G
• rs11549786
• ENST00000496871.1:n.146A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000496871.1(TES):​n.146A>G 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 0.0000331 in 1,116,726 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.000033 (0 hom.)
• Consequence: TES ENST00000496871.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 2 publications found

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]

ENSG00000279086 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BS2: High AC in GnomAdExome4 at 37 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TES	NM_015641.4	c.-2A>G		5_prime_UTR_variant	Exon 1 of 7	ENST00000358204.9	NP_056456.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TES	ENST00000358204.9	c.-2A>G		5_prime_UTR_variant	Exon 1 of 7	1	NM_015641.4	ENSP00000350937.4

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.0000331 AC: 37 AN: 1116726 Hom.: 0 Cov.: 31 AF XY: 0.0000357 AC XY: 19 AN XY: 532728

African (AFR) AF: 0.00 AC: 0 AN: 22970

American (AMR) AF: 0.00 AC: 0 AN: 9736

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15304

East Asian (EAS) AF: 0.00 AC: 0 AN: 26158

South Asian (SAS) AF: 0.00 AC: 0 AN: 26934

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37992

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4606

European-Non Finnish (NFE) AF: 0.0000398 AC: 37 AN: 928792

Other (OTH) AF: 0.00 AC: 0 AN: 44234

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.3
DANN	Benign	0.61
PhyloP100		-0.76
PromoterAI		-0.039	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs11549786; hg19: chr7-115850760;