7-116210621-C-A

Variant names:

• chr7-116210621-C-A
• rs11549785
• NM_015641.4:c.-87C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_015641.4(TES):​c.-87C>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 34)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: TES NM_015641.4 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 8 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015641.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TES	NM_015641.4	MANE Select	c.-87C>A		5_prime_UTR	Exon 1 of 7	NP_056456.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TES	ENST00000358204.9	TSL:1 MANE Select	c.-87C>A		5_prime_UTR	Exon 1 of 7	ENSP00000350937.4
	TES	ENST00000496871.1	TSL:1	n.61C>A		non_coding_transcript_exon	Exon 1 of 2
	TES	ENST00000937597.1		c.-87C>A		5_prime_UTR	Exon 1 of 7	ENSP00000607656.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1107002 Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0 AN XY: 531180

African (AFR) AF: 0.00 AC: 0 AN: 22378

American (AMR) AF: 0.00 AC: 0 AN: 9872

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14588

East Asian (EAS) AF: 0.00 AC: 0 AN: 25558

South Asian (SAS) AF: 0.00 AC: 0 AN: 31578

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38204

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4370

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 916918

Other (OTH) AF: 0.00 AC: 0 AN: 43536

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.4
DANN	Benign	0.87
PhyloP100		-0.97
PromoterAI		-0.042	Neutral
RBP_binding_hub_radar		1.0
RBP_regulation_power_radar		2.2

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

Other links and lift over

dbSNP: rs11549785; hg19: chr7-115850675;