7-116210408-T-C

Variant names:

• chr7-116210408-T-C
• rs1319886
• ENST00000624389.1:n.1104A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000624389.1(ENSG00000279086):​n.1104A>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 0.581 in 245,372 control chromosomes in the GnomAD database, including 42,441 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 (25061 hom., cov: 35)
  • Exomes 𝑓: 0.60 (17380 hom.)
• Consequence: ENSG00000279086 ENST00000624389.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.123
• Publications: 6 publications found

Genes affected

ENSG00000279086 (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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000624389.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TES	NM_015641.4	MANE Select	c.-300T>C		upstream_gene	N/A	NP_056456.1	A4D0U5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000279086	ENST00000624389.1	TSL:6	n.1104A>G		non_coding_transcript_exon	Exon 1 of 1
	TES	ENST00000358204.9	TSL:1 MANE Select	c.-300T>C		upstream_gene	N/A	ENSP00000350937.4	Q9UGI8-1
	TES	ENST00000496871.1	TSL:1	n.-153T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86384 AN: 151968 Hom.: 25010 Cov.: 35

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.578

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 0.601 AC: 56047 AN: 93294 Hom.: 17380 Cov.: 0 AF XY: 0.600 AC XY: 28505 AN XY: 47500

African (AFR) AF: 0.497 AC: 1382 AN: 2780

American (AMR) AF: 0.675 AC: 1646 AN: 2438

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1731 AN: 3394

East Asian (EAS) AF: 0.879 AC: 7298 AN: 8300

South Asian (SAS) AF: 0.568 AC: 487 AN: 858

European-Finnish (FIN) AF: 0.581 AC: 5193 AN: 8936

Middle Eastern (MID) AF: 0.573 AC: 307 AN: 536

European-Non Finnish (NFE) AF: 0.574 AC: 34464 AN: 60052

Other (OTH) AF: 0.590 AC: 3539 AN: 6000

GnomAD4 genome AF: 0.569 AC: 86487 AN: 152078 Hom.: 25061 Cov.: 35 AF XY: 0.575 AC XY: 42757 AN XY: 74358

African (AFR) AF: 0.495 AC: 20562 AN: 41516

American (AMR) AF: 0.636 AC: 9721 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.521 AC: 1808 AN: 3468

East Asian (EAS) AF: 0.856 AC: 4414 AN: 5156

South Asian (SAS) AF: 0.597 AC: 2887 AN: 4834

European-Finnish (FIN) AF: 0.590 AC: 6232 AN: 10566

Middle Eastern (MID) AF: 0.565 AC: 165 AN: 292

European-Non Finnish (NFE) AF: 0.574 AC: 39023 AN: 67940

Other (OTH) AF: 0.545 AC: 1151 AN: 2110

Alfa AF: 0.573 Hom.: 3110

Bravo AF: 0.568

Asia WGS AF: 0.710 AC: 2464 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	17
DANN	Benign	0.65
PhyloP100		0.12
PromoterAI		0.16	Neutral
Mutation Taster		=100/0	polymorphism

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1319886;

hg19: chr7-115850462;

COSMIC: COSV64043800;